rs6967345

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 0.634 in 152,132 control chromosomes in the GnomAD database, including 31,422 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 0.63 ( 31422 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.973
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.634
AC:
96343
AN:
152014
Hom.:
31394
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.720
Gnomad AMI
AF:
0.666
Gnomad AMR
AF:
0.580
Gnomad ASJ
AF:
0.582
Gnomad EAS
AF:
0.273
Gnomad SAS
AF:
0.338
Gnomad FIN
AF:
0.692
Gnomad MID
AF:
0.624
Gnomad NFE
AF:
0.635
Gnomad OTH
AF:
0.634
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.634
AC:
96427
AN:
152132
Hom.:
31422
Cov.:
33
AF XY:
0.628
AC XY:
46697
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.721
Gnomad4 AMR
AF:
0.580
Gnomad4 ASJ
AF:
0.582
Gnomad4 EAS
AF:
0.273
Gnomad4 SAS
AF:
0.336
Gnomad4 FIN
AF:
0.692
Gnomad4 NFE
AF:
0.635
Gnomad4 OTH
AF:
0.631
Alfa
AF:
0.626
Hom.:
37548
Bravo
AF:
0.631
Asia WGS
AF:
0.375
AC:
1305
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.5
DANN
Benign
0.42

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: rs6967345; hg19: chr7-53156188; API