6-31291802-C-T

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 0.657 in 151,988 control chromosomes in the GnomAD database, including 33,175 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 0.66 ( 33175 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.56
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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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:
0.657
AC:
99824
AN:
151870
Hom.:
33134
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.735
Gnomad AMI
AF:
0.483
Gnomad AMR
AF:
0.718
Gnomad ASJ
AF:
0.581
Gnomad EAS
AF:
0.720
Gnomad SAS
AF:
0.688
Gnomad FIN
AF:
0.669
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.594
Gnomad OTH
AF:
0.682
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.657
AC:
99918
AN:
151988
Hom.:
33175
Cov.:
31
AF XY:
0.662
AC XY:
49192
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.735
Gnomad4 AMR
AF:
0.718
Gnomad4 ASJ
AF:
0.581
Gnomad4 EAS
AF:
0.721
Gnomad4 SAS
AF:
0.688
Gnomad4 FIN
AF:
0.669
Gnomad4 NFE
AF:
0.594
Gnomad4 OTH
AF:
0.682
Alfa
AF:
0.602
Hom.:
22995
Bravo
AF:
0.666
Asia WGS
AF:
0.714
AC:
2482
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.6
DANN
Benign
0.16

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: rs2524163; hg19: chr6-31259579; API