6-31273182-C-G

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 0.264 in 151,792 control chromosomes in the GnomAD database, including 5,440 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 0.26 ( 5440 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91
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=-1.01).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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:
0.264
AC:
39996
AN:
151672
Hom.:
5438
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.228
Gnomad AMI
AF:
0.374
Gnomad AMR
AF:
0.251
Gnomad ASJ
AF:
0.524
Gnomad EAS
AF:
0.225
Gnomad SAS
AF:
0.335
Gnomad FIN
AF:
0.174
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.285
Gnomad OTH
AF:
0.282
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.264
AC:
39999
AN:
151792
Hom.:
5440
Cov.:
31
AF XY:
0.260
AC XY:
19317
AN XY:
74192
show subpopulations
Gnomad4 AFR
AF:
0.228
Gnomad4 AMR
AF:
0.251
Gnomad4 ASJ
AF:
0.524
Gnomad4 EAS
AF:
0.225
Gnomad4 SAS
AF:
0.333
Gnomad4 FIN
AF:
0.174
Gnomad4 NFE
AF:
0.285
Gnomad4 OTH
AF:
0.278
Alfa
AF:
0.0763
Hom.:
91
Bravo
AF:
0.266
Asia WGS
AF:
0.268
AC:
933
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
0.048
DANN
Benign
0.31

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: rs7773175; hg19: chr6-31240959; API