2-67843093-A-G

Variant names:

• chr2-67843093-A-G
• rs6747972

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 0.65 in 152,110 control chromosomes in the GnomAD database, including 33,605 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 0.65 (33605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 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: 0.650 AC: 98802 AN: 151990 Hom.: 33562 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.650 AC: 98900 AN: 152110 Hom.: 33605 Cov.: 32 AF XY: 0.646 AC XY: 48029 AN XY: 74358

African (AFR) AF: 0.866 AC: 35974 AN: 41522

American (AMR) AF: 0.535 AC: 8192 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3466

East Asian (EAS) AF: 0.624 AC: 3226 AN: 5172

South Asian (SAS) AF: 0.610 AC: 2938 AN: 4820

European-Finnish (FIN) AF: 0.576 AC: 6081 AN: 10558

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38431 AN: 67966

Other (OTH) AF: 0.622 AC: 1309 AN: 2106

Alfa AF: 0.595 Hom.: 86417

Bravo AF: 0.660

Asia WGS AF: 0.659 AC: 2293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.041
DANN	Benign	0.63
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6747972; hg19: chr2-68070225;