rs1813617

Variant names:

• chr2-19390258-C-A
• rs1813617

Your query was ambiguous. Multiple possible variants found:

• chr2-19390258-C-A
• chr2-19390258-C-G
• chr2-19390258-C-T

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 0.452 in 151,886 control chromosomes in the GnomAD database, including 16,291 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 0.45 (16291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.452 AC: 68593 AN: 151768 Hom.: 16259 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.452 AC: 68686 AN: 151886 Hom.: 16291 Cov.: 32 AF XY: 0.461 AC XY: 34196 AN XY: 74230

African (AFR) AF: 0.454 AC: 18809 AN: 41392

American (AMR) AF: 0.577 AC: 8801 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3468

East Asian (EAS) AF: 0.870 AC: 4496 AN: 5168

South Asian (SAS) AF: 0.475 AC: 2285 AN: 4810

European-Finnish (FIN) AF: 0.471 AC: 4966 AN: 10540

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26478 AN: 67944

Other (OTH) AF: 0.476 AC: 1002 AN: 2104

Alfa AF: 0.408 Hom.: 47952

Bravo AF: 0.462

Asia WGS AF: 0.682 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1813617; hg19: chr2-19590019;