rs7581219

Variant names:

• chr2-173498846-G-A
• rs7581219

Your query was ambiguous. Multiple possible variants found:

• chr2-173498846-G-A
• chr2-173498846-G-C

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 0.387 in 151,986 control chromosomes in the GnomAD database, including 11,516 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 0.39 (11516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58814 AN: 151868 Hom.: 11517 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.387 AC: 58832 AN: 151986 Hom.: 11516 Cov.: 32 AF XY: 0.382 AC XY: 28393 AN XY: 74280

African (AFR) AF: 0.430 AC: 17807 AN: 41454

American (AMR) AF: 0.362 AC: 5529 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1593 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1648 AN: 5170

South Asian (SAS) AF: 0.387 AC: 1858 AN: 4804

European-Finnish (FIN) AF: 0.282 AC: 2975 AN: 10562

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25934 AN: 67946

Other (OTH) AF: 0.421 AC: 887 AN: 2108

Alfa AF: 0.377 Hom.: 7221

Bravo AF: 0.396

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7581219; hg19: chr2-174363574;