6-31106253-A-C

Variant names:

• chr6-31106253-A-C
• rs6457327

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.656 in 151,988 control chromosomes in the GnomAD database, including 33,023 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 (33023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 90 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99666 AN: 151870 Hom.: 32989 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.696

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.656 AC: 99741 AN: 151988 Hom.: 33023 Cov.: 31 AF XY: 0.655 AC XY: 48639 AN XY: 74264

African (AFR) AF: 0.722 AC: 29932 AN: 41464

American (AMR) AF: 0.609 AC: 9292 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2934 AN: 3470

East Asian (EAS) AF: 0.644 AC: 3320 AN: 5156

South Asian (SAS) AF: 0.729 AC: 3509 AN: 4812

European-Finnish (FIN) AF: 0.606 AC: 6392 AN: 10542

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 41998 AN: 67960

Other (OTH) AF: 0.691 AC: 1459 AN: 2110

Alfa AF: 0.634 Hom.: 112379

Bravo AF: 0.658

Asia WGS AF: 0.670 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.75
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6457327; hg19: chr6-31074030;