15-43610999-GT-GTTT

Position:

• chr15-43610999-GT-GTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_153700.2(STRC):​c.3307-17_3307-16dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000813 in 1,279,084 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00018 (1 hom., cov: 23)
  • Exomes 𝑓: 0.000075 (1 hom.)
• Consequence: STRC NM_153700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

Genes affected

STRC (HGNC:16035): (stereocilin) This gene encodes a protein that is associated with the hair bundle of the sensory hair cells in the inner ear. The hair bundle is composed of stiff microvilli called stereocilia and is involved with mechanoreception of sound waves. This gene is part of a tandem duplication on chromosome 15; the second copy is a pseudogene. Mutations in this gene cause autosomal recessive non-syndromic deafness. [provided by RefSeq, Jul 2008]

STRC (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRC	NM_153700.2	c.3307-17_3307-16dupAA		intron_variant		ENST00000450892.7	NP_714544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRC	ENST00000450892.7	c.3307-17_3307-16dupAA		intron_variant		5	NM_153700.2	ENSP00000401513.2

Frequencies

GnomAD3 genomes AF: 0.000185 AC: 14 AN: 75776 Hom.: 1 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000122

Gnomad ASJ AF: 0.000575

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00449

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000244

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000748 AC: 90 AN: 1203274 Hom.: 1 Cov.: 61 AF XY: 0.000110 AC XY: 66 AN XY: 602336

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000287

Gnomad4 ASJ exome AF: 0.0000967

Gnomad4 EAS exome AF: 0.0000277

Gnomad4 SAS exome AF: 0.00100

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000657

Gnomad4 OTH exome AF: 0.000100

GnomAD4 genome AF: 0.000185 AC: 14 AN: 75810 Hom.: 1 Cov.: 23 AF XY: 0.000319 AC XY: 12 AN XY: 37676

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000121

Gnomad4 ASJ AF: 0.000575

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00448

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000244

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727503445; hg19: chr15-43903197;