rs963274

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 0.102 in 152,032 control chromosomes in the GnomAD database, including 1,170 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 0.10 ( 1170 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.56
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15553
AN:
151912
Hom.:
1169
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.00989
Gnomad AMR
AF:
0.0890
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0230
Gnomad FIN
AF:
0.0308
Gnomad MID
AF:
0.143
Gnomad NFE
AF:
0.0689
Gnomad OTH
AF:
0.114
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15570
AN:
152032
Hom.:
1170
Cov.:
32
AF XY:
0.0983
AC XY:
7308
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.202
Gnomad4 AMR
AF:
0.0889
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.0228
Gnomad4 FIN
AF:
0.0308
Gnomad4 NFE
AF:
0.0689
Gnomad4 OTH
AF:
0.112
Alfa
AF:
0.0813
Hom.:
138
Bravo
AF:
0.113
Asia WGS
AF:
0.0230
AC:
81
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
0.024
DANN
Benign
0.51

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: rs963274; hg19: chr6-50374111; API