chr11-17526492-G-A

Variant names:

• chr11-17526492-G-A
• rs36001077
• NM_153676.4:c.580-51C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_153676.4(USH1C):​c.580-51C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 1,522,388 control chromosomes in the GnomAD database, including 181 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.010 (8 hom., cov: 33)
  • Exomes 𝑓: 0.014 (173 hom.)
• Consequence: USH1C NM_153676.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 1 publications found

Genes affected

USH1C (HGNC:12597): (USH1 protein network component harmonin) This gene encodes a scaffold protein that functions in the assembly of Usher protein complexes. The protein contains PDZ domains, a coiled-coil region with a bipartite nuclear localization signal and a PEST degradation sequence. Defects in this gene are the cause of Usher syndrome type 1C and non-syndromic sensorineural deafness autosomal recessive type 18. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

USH1C Gene-Disease associations (from GenCC):

• Usher syndrome type 1

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• Usher syndrome type 1C

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics, PanelApp Australia
• autosomal recessive nonsyndromic hearing loss 18A

  Inheritance: AR, Unknown Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0104 (1581/152278) while in subpopulation NFE AF = 0.0164 (1112/68006). AF 95% confidence interval is 0.0156. There are 8 homozygotes in GnomAd4. There are 738 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 8 AR,Unknown gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USH1C	NM_153676.4	c.580-51C>T		intron_variant	Intron 7 of 26	ENST00000005226.12	NP_710142.1
USH1C	NM_005709.4	c.580-51C>T		intron_variant	Intron 7 of 20	ENST00000318024.9	NP_005700.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USH1C	ENST00000005226.12	c.580-51C>T		intron_variant	Intron 7 of 26	5	NM_153676.4	ENSP00000005226.7
USH1C	ENST00000318024.9	c.580-51C>T		intron_variant	Intron 7 of 20	1	NM_005709.4	ENSP00000317018.4

Frequencies

GnomAD3 genomes AF: 0.0104 AC: 1579 AN: 152160 Hom.: 8 Cov.: 33

Gnomad AFR AF: 0.00186

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00648

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00289

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.00621

GnomAD2 exomes AF: 0.0108 AC: 2386 AN: 220892 AF XY: 0.0108

Gnomad AFR exome AF: 0.00205

Gnomad AMR exome AF: 0.00464

Gnomad ASJ exome AF: 0.0113

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0205

Gnomad NFE exome AF: 0.0160

Gnomad OTH exome AF: 0.0114

GnomAD4 exome AF: 0.0142 AC: 19505 AN: 1370110 Hom.: 173 Cov.: 21 AF XY: 0.0142 AC XY: 9704 AN XY: 684972

African (AFR) AF: 0.00149 AC: 47 AN: 31620

American (AMR) AF: 0.00461 AC: 194 AN: 42108

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 307 AN: 25314

East Asian (EAS) AF: 0.0000518 AC: 2 AN: 38642

South Asian (SAS) AF: 0.00391 AC: 324 AN: 82804

European-Finnish (FIN) AF: 0.0225 AC: 1143 AN: 50884

Middle Eastern (MID) AF: 0.00249 AC: 14 AN: 5612

European-Non Finnish (NFE) AF: 0.0162 AC: 16815 AN: 1035862

Other (OTH) AF: 0.0115 AC: 659 AN: 57264

GnomAD4 genome AF: 0.0104 AC: 1581 AN: 152278 Hom.: 8 Cov.: 33 AF XY: 0.00991 AC XY: 738 AN XY: 74464

African (AFR) AF: 0.00185 AC: 77 AN: 41554

American (AMR) AF: 0.00647 AC: 99 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 40 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.00310 AC: 15 AN: 4832

European-Finnish (FIN) AF: 0.0208 AC: 221 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1112 AN: 68006

Other (OTH) AF: 0.00614 AC: 13 AN: 2116

Alfa AF: 0.0166 Hom.: 3

Bravo AF: 0.00833

Asia WGS AF: 0.00375 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs36001077; hg19: chr11-17548039;