6-31050630-A-G

Variant names:

• chr6-31050630-A-G
• rs2517532

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 0.598 in 152,044 control chromosomes in the GnomAD database, including 27,441 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 0.60 (27441 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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: 0.598 AC: 90864 AN: 151926 Hom.: 27412 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.598 AC: 90940 AN: 152044 Hom.: 27441 Cov.: 33 AF XY: 0.594 AC XY: 44147 AN XY: 74316

African (AFR) AF: 0.664 AC: 27548 AN: 41490

American (AMR) AF: 0.569 AC: 8678 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2580 AN: 5178

South Asian (SAS) AF: 0.574 AC: 2763 AN: 4814

European-Finnish (FIN) AF: 0.562 AC: 5925 AN: 10534

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38685 AN: 67982

Other (OTH) AF: 0.643 AC: 1357 AN: 2112

Alfa AF: 0.583 Hom.: 97611

Bravo AF: 0.602

Asia WGS AF: 0.528 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.69
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2517532; hg19: chr6-31018407;