rs60284988

Positions:

• chr7-107660756-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NR_028137.1(SLC26A4-AS1):​n.198-550A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.00201 in 152,334 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★).

• Frequency:
  • Genomes: 𝑓 0.0020 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC26A4-AS1 NR_028137.1 intron, non_coding_transcript
• Clinical Significance: Uncertain significance reviewed by expert panel P:3 U:8 B:1
• Conservation: PhyloP100: 3.81

Genes affected

SLC26A4-AS1 (HGNC:22385): (SLC26A4 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BS2: High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC26A4-AS1	NR_028137.1	n.198-550A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A4-AS1	ENST00000668981.1	n.257+846A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00201 AC: 306 AN: 152216 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.000169

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00385

Gnomad OTH AF: 0.00191

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 48 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 38

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00201 AC: 306 AN: 152334 Hom.: 4 Cov.: 32 AF XY: 0.00162 AC XY: 121 AN XY: 74486

Gnomad4 AFR AF: 0.000168

Gnomad4 AMR AF: 0.000458

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00141

Gnomad4 NFE AF: 0.00385

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00210 Hom.: 0

Bravo AF: 0.00177

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:3 Uncertain:8 Benign:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Uncertain:4 Benign:1

Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The SLC26A4 c.103T>C variant was identified as a heterozygous variant in 14 of 674 individuals (frequency: 0.01) with autosomal recessive Pendred syndrome or nonsyndromic hearing loss associated with enlarged vestibular aqueduct (EVA); a second pathogenic variant was only identified in 3 of these cases (Carvalho_2018_PMID:30068397, Yang_2007_PMID:17503324, Choi_2009_PMID:19204907, Tang_2015_PMID:2599145). Functional analysis shows that this variant diminishes FOXI1 transactivation of SLC26A4 compared to wildtype (Yang_2007_PMID:17503324). The variant was identified in dbSNP (ID: rs60284988), LOVD 3.0 and ClinVar (classified as uncertain significance by the ClinGen Hearing Loss Variant Curation Expert Panel, Counsyl, Laboratory for Molecular Medicine and Illumina, and as likely pathogenic by GeneDx). The variant was identified in control databases in 66 of 31390 chromosomes at a frequency of 0.002103 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Other in 6 of 1086 chromosomes (freq: 0.005525), Ashkenazi Jewish in 1 of 290 chromosomes (freq: 0.003448), European (non-Finnish) in 52 of 15424 chromosomes (freq: 0.003371), European (Finnish) in 4 of 3476 chromosomes (freq: 0.001151) and African in 3 of 8708 chromosomes (freq: 0.000345), but was not observed in the Latino, East Asian, or South Asian populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this timet. This variant is classified as a variant of uncertain significance. -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2023	Classified as a variant of uncertain significance by the ClinGen Hearing Loss Expert Panel (ClinVar SCV000927013.1; Oza et al., 2018); This variant is associated with the following publications: (PMID: 25910213, 19787632, 24860705, 22285650, 23208854, 18322141, 23555729, 21045265, 30068397, 29196752, 31633822, 28780564, 25960948, 34426522, 25991456, 23965030, 17503324, 19204907) -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Sep 21, 2023	- -

Pendred syndrome Pathogenic:1 Uncertain:2

Uncertain significance, reviewed by expert panel	curation	ClinGen Hearing Loss Variant Curation Expert Panel	Jan 17, 2024	The c.-103T>C (NM_000441.2) variant is a substitution in the 5’ UTR of SLC26A4. Because the variant is located in the 5’ UTR, it is not expected to alter the amino acid sequence. The highest population minor allele frequency in gnomAD v4.0.0 is 0.3% (262/68066 alleles) in the European (non-Finnish) population, which is a high enough frequency to be classified as likely benign based on the thresholds defined by the ClinGen Hearing Loss Expert Panel (HL EP) for autosomal recessive hearing loss variants (BS1). This variant has been detected in 2 individuals with hearing loss and additional features of Pendred syndrome (enlarged vestibular aqueducts (EVA) and Mondini dysplasia) who were compound heterozygous for the variant and a pathogenic variant with phase confirmed in trans in one individual (PMID: 19204907, 25991456). It has also been identified in two additional compound heterozygous individuals with hearing loss, one with a likely pathogenic and one with a variant of uncertain significance, though phase was not confirmed in either individual (SCV000491274.5). However, due to the allele frequency meeting BS1 criteria, PP4 and PM3 were not applied. There have been many reported heterozygous observations in individuals with EVA/Pendred syndrome (PMID:17503324, 23208854, 23965030, 25991456). Functional studies imply that the variant occurs in a binding site that is a major transcriptional regulatory element of SLC26A4 and is necessary for FOXI1-induced transcriptional activation of SLC26A4 (PMID:25910213, 17503324; PS3_Supporting). Due to conflicting evidence, this variant is classified as a variant of uncertain significance for autosomal recessive Pendred syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: BS1, PS3_P (ClinGen Hearing Loss VCEP specifications version 2; 01/17/2024). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 2007	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Oct 01, 2021	NM_000441.1(SLC26A4):c.-103T>C is a 5' non-coding variant classified as a variant of uncertain significance in the context of Pendred syndrome. c.-103T>C has been observed in cases with relevant disease (PMID: 17503324, 19204907, 23208854, 23555729, 23965030, 25991456, 31633822, 30068397). Functional assessments of this variant are available in the literature (PMID: 17503324). c.-103T>C has been observed in population frequency databases (gnomAD: NFE 0.34%). In summary, there is insufficient evidence to classify NM_000441.1(SLC26A4):c.-103T>C as pathogenic or benign. Please note: this variant was assessed in the context of healthy population screening. -

Autosomal recessive nonsyndromic hearing loss 4 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 01, 2007

- -

Hearing impairment Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Department of Otolaryngology – Head & Neck Surgery, Cochlear Implant Center

Apr 12, 2021

PS1_Strong, PM2_Supporting, BP4_Supporting -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Feb 26, 2019

The c.-103T>C variant in SLC26A4 has been reported in >20 individuals with either hearing loss or hearing loss with enlarged vestibular aqueducts (EVA; Yang 2007, Yang 2009, Choi 2009, Landa 2013, Schrauwen 2013, Tang 2015, Baux 2017, Carvalho 2018, LMM data). However, only 2 of these individuals harbored a second pathogenic variant in SLC26A4, including one individual with hearing loss and EVA who carried a pathogenic p.Leu236Pro variant in trans (Choi 2009) and one individual with hearing loss and Mondini malformation who carried a pathogenic p.Thr416Pro variant (phasing not reported; Tang 2015). Furthermore, at least 3 probands had alternate genetic etiologies for their hearing loss (LMM data, Baux 2017). This variant has also been identified in 0.34% (52/15424; 0.26% using the lower threshold of 95% confidence interval) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This frequency is higher than expected for pathogenic variation in SLC26A4. Finally, the c.-103T>C variant falls within the 5' untranslated region (UTR) of the SLC26A4 gene, and functional studies have produced conflicting results regarding its impact on protein expression or function (Alder 2008 vs Yang 2007, Yang 2009). In summary, due to the conflicting functional evidence, the lack of biallelic affected individuals, and a similar frequency amongst cases (0.3%, 23/6678 chromosomes) and the general population (0.3% European chromosomes in gnomAD), the clinical significance of the c.-103T>C variant is uncertain. ACMG/AMP criteria applied: BS1_Supporting, PM3, PP4, PS3_Supporting. -

SLC26A4-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 05, 2019

The SLC26A4 c.-103T>C 5' UTR variant has been reported in at least four studies in which it was found in a total of 14 individuals with clinical features of Pendred syndrome or isolated hearing loss/impairment or nonsyndromic enlarged vestibular aqueduct. Among these individuals, the variant was identified in a compound heterozygous state in one individual, in conjunction with a second missense variant in one individual (phase unknown), and in a heterozygous state in 12 individuals (Yang et al. 2007; Choi et al. 2009; Landa et al. 2013; Tang et al. 2015). Although SLC26A4-related disorders are inherited in an autosomal recessive manner, it is not uncommon to detect a single disease-causing variant in patients due to testing limitations and biological complexities. Frequency information for the c.-103T>C variant is not available from the 1000 Genomes Project, the Exome Sequencing Project or the Exome Aggregation Consortium; however, the variant was absent from 452 control chromosomes (Yang et al. 2007; Choi et al. 2009). A luciferase promotor-reporter expression assay showed the variant reduces FOXI1 binding affinity and abolishes FOXI1-mediated transcriptional activation of SLC26A4 (Yang et al. 2007). Evidence for this variant is limited, therefore, the c.-103T>C variant is classified as a variant of unknown significance but suspicious for pathogenicity for SLC26A4-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	22
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs60284988; hg19: chr7-107301201;