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GeneBe

rs4979416

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015404.4(WHRN):c.618+3587C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,178 control chromosomes in the GnomAD database, including 1,811 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 0.13 ( 1811 hom., cov: 32)

Consequence

WHRN
NM_015404.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390
Variant links:
Genes affected
WHRN (HGNC:16361): (whirlin) This gene is thought to function in the organization and stabilization of sterocilia elongation and actin cystoskeletal assembly, based on studies of the related mouse gene. Mutations in this gene have been associated with autosomal recessive non-syndromic deafness and Usher Syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WHRNNM_015404.4 linkuse as main transcriptc.618+3587C>T intron_variant ENST00000362057.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WHRNENST00000362057.4 linkuse as main transcriptc.618+3587C>T intron_variant 1 NM_015404.4 P1Q9P202-1

Frequencies

GnomAD3 genomes
AF:
0.132
AC:
20034
AN:
152060
Hom.:
1799
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.202
Gnomad AMI
AF:
0.175
Gnomad AMR
AF:
0.172
Gnomad ASJ
AF:
0.152
Gnomad EAS
AF:
0.357
Gnomad SAS
AF:
0.224
Gnomad FIN
AF:
0.0948
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.0605
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.132
AC:
20082
AN:
152178
Hom.:
1811
Cov.:
32
AF XY:
0.138
AC XY:
10285
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.173
Gnomad4 ASJ
AF:
0.152
Gnomad4 EAS
AF:
0.357
Gnomad4 SAS
AF:
0.224
Gnomad4 FIN
AF:
0.0948
Gnomad4 NFE
AF:
0.0605
Gnomad4 OTH
AF:
0.123
Alfa
AF:
0.101
Hom.:
214
Bravo
AF:
0.142
Asia WGS
AF:
0.265
AC:
918
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
Cadd
Benign
1.3
Dann
Benign
0.50

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4979416; hg19: chr9-117262877; API