chr2-181443625-A-G

Variant names:

• chr2-181443625-A-G
• rs6740847

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 0.57 in 151,846 control chromosomes in the GnomAD database, including 25,304 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 0.57 (25304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 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: 0.570 AC: 86549 AN: 151728 Hom.: 25283 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.570 AC: 86608 AN: 151846 Hom.: 25304 Cov.: 32 AF XY: 0.572 AC XY: 42425 AN XY: 74184

African (AFR) AF: 0.636 AC: 26341 AN: 41444

American (AMR) AF: 0.499 AC: 7626 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1709 AN: 5150

South Asian (SAS) AF: 0.613 AC: 2947 AN: 4806

European-Finnish (FIN) AF: 0.622 AC: 6546 AN: 10516

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37899 AN: 67878

Other (OTH) AF: 0.553 AC: 1169 AN: 2114

Alfa AF: 0.554 Hom.: 100174

Bravo AF: 0.562

Asia WGS AF: 0.472 AC: 1637 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6740847; hg19: chr2-182308352;