rs6956675

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 0.793 in 227,688 control chromosomes in the GnomAD database, including 72,003 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 0.78 ( 47024 hom., cov: 32)
Exomes 𝑓: 0.81 ( 24979 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.51
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=-1.07).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 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:
0.783
AC:
119008
AN:
151940
Hom.:
46970
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.882
Gnomad AMI
AF:
0.604
Gnomad AMR
AF:
0.829
Gnomad ASJ
AF:
0.727
Gnomad EAS
AF:
0.778
Gnomad SAS
AF:
0.762
Gnomad FIN
AF:
0.775
Gnomad MID
AF:
0.739
Gnomad NFE
AF:
0.722
Gnomad OTH
AF:
0.768
GnomAD4 exome
AF:
0.812
AC:
61385
AN:
75630
Hom.:
24979
AF XY:
0.810
AC XY:
34602
AN XY:
42724
show subpopulations
Gnomad4 AFR exome
AF:
0.915
Gnomad4 AMR exome
AF:
0.893
Gnomad4 ASJ exome
AF:
0.804
Gnomad4 EAS exome
AF:
0.828
Gnomad4 SAS exome
AF:
0.828
Gnomad4 FIN exome
AF:
0.831
Gnomad4 NFE exome
AF:
0.797
Gnomad4 OTH exome
AF:
0.816
GnomAD4 genome
AF:
0.783
AC:
119119
AN:
152058
Hom.:
47024
Cov.:
32
AF XY:
0.786
AC XY:
58432
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.882
Gnomad4 AMR
AF:
0.829
Gnomad4 ASJ
AF:
0.727
Gnomad4 EAS
AF:
0.778
Gnomad4 SAS
AF:
0.763
Gnomad4 FIN
AF:
0.775
Gnomad4 NFE
AF:
0.722
Gnomad4 OTH
AF:
0.768
Alfa
AF:
0.735
Hom.:
48717
Bravo
AF:
0.793
Asia WGS
AF:
0.786
AC:
2732
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.27
DANN
Benign
0.45

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: rs6956675; hg19: chr7-62577770; API