rs179913

Variant summary

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

The variant allele was found at a frequency of 0.24 in 152,128 control chromosomes in the GnomAD database, including 5,327 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 0.24 ( 5327 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.335
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.240
AC:
36440
AN:
152010
Hom.:
5327
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0865
Gnomad AMI
AF:
0.229
Gnomad AMR
AF:
0.245
Gnomad ASJ
AF:
0.297
Gnomad EAS
AF:
0.0405
Gnomad SAS
AF:
0.195
Gnomad FIN
AF:
0.306
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.337
Gnomad OTH
AF:
0.254
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.240
AC:
36445
AN:
152128
Hom.:
5327
Cov.:
32
AF XY:
0.236
AC XY:
17585
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0866
Gnomad4 AMR
AF:
0.245
Gnomad4 ASJ
AF:
0.297
Gnomad4 EAS
AF:
0.0404
Gnomad4 SAS
AF:
0.194
Gnomad4 FIN
AF:
0.306
Gnomad4 NFE
AF:
0.337
Gnomad4 OTH
AF:
0.251
Alfa
AF:
0.313
Hom.:
8580
Bravo
AF:
0.225
Asia WGS
AF:
0.115
AC:
401
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.46
DANN
Benign
0.66

Splicing

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: rs179913; hg19: chr17-67903643; API