6-31218468-A-G

Variant names:

• chr6-31218468-A-G
• rs9263967

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 0.589 in 152,146 control chromosomes in the GnomAD database, including 26,575 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 0.59 (26575 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89582 AN: 152028 Hom.: 26546 Cov.: 33

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.589 AC: 89657 AN: 152146 Hom.: 26575 Cov.: 33 AF XY: 0.594 AC XY: 44210 AN XY: 74380

African (AFR) AF: 0.608 AC: 25223 AN: 41514

American (AMR) AF: 0.622 AC: 9507 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2296 AN: 5170

South Asian (SAS) AF: 0.529 AC: 2554 AN: 4826

European-Finnish (FIN) AF: 0.669 AC: 7068 AN: 10572

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38807 AN: 68004

Other (OTH) AF: 0.611 AC: 1289 AN: 2110

Alfa AF: 0.574 Hom.: 43065

Bravo AF: 0.590

Asia WGS AF: 0.567 AC: 1971 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	3.0
DANN	Benign	0.37
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9263967; hg19: chr6-31186245;