rs45466695

chr5-170109535-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_012188.5(FOXI1):c.*924C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 137,108 control chromosomes in the GnomAD database, including 270 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.055 (270 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FOXI1 NM_012188.5 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.40

Genes affected

FOXI1 (HGNC:3815): (forkhead box I1) This gene belongs to the forkhead family of transcription factors, which is characterized by a distinct forkhead domain. This gene may play an important role in the development of the cochlea and vestibulum, as well as in embryogenesis. The encoded protein has been found to be required for the transcription of four subunits of a proton pump found in the inner ear, the kidney, and the epididymis. Mutations in this gene have been associated with deafness, autosomal recessive 4. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 5-170109535-C-T is Benign according to our data. Variant chr5-170109535-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 905992.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXI1	NM_012188.5	c.*924C>T		3_prime_UTR_variant	2/2	ENST00000306268.8
FOXI1	NM_144769.4	c.*924C>T		3_prime_UTR_variant	2/2
FOXI1	XR_941092.2	n.2267C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXI1	ENST00000306268.8	c.*924C>T		3_prime_UTR_variant	2/2	1	NM_012188.5	P1
FOXI1	ENST00000449804.4	c.*924C>T		3_prime_UTR_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 7592 AN: 137038 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0382

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0388

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0229

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.0483

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0554 AC: 7595 AN: 137108 Hom.: 270 Cov.: 32 AF XY: 0.0578 AC XY: 3875 AN XY: 67012

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.0447

Gnomad4 ASJ AF: 0.0388

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0672

Gnomad4 OTH AF: 0.0480

Alfa AF: 0.0646 Hom.: 95

Bravo AF: 0.0420

Asia WGS AF: 0.0420 AC: 148 AN: 3472

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Autosomal recessive nonsyndromic hearing loss 4 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45466695; hg19: chr5-169536539;