chr6-31103281-A-C

Variant names:

• chr6-31103281-A-C
• rs2508011

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 0.369 in 151,904 control chromosomes in the GnomAD database, including 10,752 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 0.37 (10752 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55973 AN: 151786 Hom.: 10740 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.369 AC: 56016 AN: 151904 Hom.: 10752 Cov.: 31 AF XY: 0.365 AC XY: 27141 AN XY: 74280

African (AFR) AF: 0.445 AC: 18409 AN: 41396

American (AMR) AF: 0.358 AC: 5468 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1923 AN: 3466

East Asian (EAS) AF: 0.100 AC: 518 AN: 5180

South Asian (SAS) AF: 0.313 AC: 1502 AN: 4800

European-Finnish (FIN) AF: 0.368 AC: 3889 AN: 10578

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 22998 AN: 67906

Other (OTH) AF: 0.403 AC: 851 AN: 2110

Alfa AF: 0.364 Hom.: 8174

Bravo AF: 0.373

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2508011; hg19: chr6-31071058;