7-107683668-G-T

Position:

• chr7-107683668-G-T

Variant summary

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

The NM_000441.2(SLC26A4):​c.1001+131G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 753,910 control chromosomes in the GnomAD database, including 201,393 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.75 (43558 hom., cov: 32)
  • Exomes 𝑓: 0.72 (157835 hom.)
• Consequence: SLC26A4 NM_000441.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.230

Genes affected

SLC26A4 (HGNC:8818): (solute carrier family 26 member 4) Mutations in this gene are associated with Pendred syndrome, the most common form of syndromic deafness, an autosomal-recessive disease. It is highly homologous to the SLC26A3 gene; they have similar genomic structures and this gene is located 3' of the SLC26A3 gene. The encoded protein has homology to sulfate transporters. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 7-107683668-G-T is Benign according to our data. Variant chr7-107683668-G-T is described in ClinVar as [Benign]. Clinvar id is 1236994.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC26A4	NM_000441.2	c.1001+131G>T		intron_variant		ENST00000644269.2	NP_000432.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC26A4	ENST00000644269.2	c.1001+131G>T		intron_variant			NM_000441.2	ENSP00000494017.1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114454 AN: 151904 Hom.: 43545 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.751

GnomAD4 exome AF: 0.721 AC: 434121 AN: 601888 Hom.: 157835 AF XY: 0.715 AC XY: 227094 AN XY: 317426

Gnomad4 AFR exome AF: 0.858

Gnomad4 AMR exome AF: 0.641

Gnomad4 ASJ exome AF: 0.733

Gnomad4 EAS exome AF: 0.630

Gnomad4 SAS exome AF: 0.590

Gnomad4 FIN exome AF: 0.689

Gnomad4 NFE exome AF: 0.748

Gnomad4 OTH exome AF: 0.734

GnomAD4 genome AF: 0.753 AC: 114516 AN: 152022 Hom.: 43558 Cov.: 32 AF XY: 0.743 AC XY: 55211 AN XY: 74280

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.748

Alfa AF: 0.732 Hom.: 33990

Bravo AF: 0.760

Asia WGS AF: 0.587 AC: 2046 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.56

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: rs2395911; hg19: chr7-107324113;