rs1515104

Variant names:

• chr2-226227689-T-A
• rs1515104

Your query was ambiguous. Multiple possible variants found:

• chr2-226227689-T-A
• chr2-226227689-T-C
• chr2-226227689-T-G

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 0.724 in 152,046 control chromosomes in the GnomAD database, including 40,447 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 0.72 (40447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.724 AC: 109948 AN: 151928 Hom.: 40394 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.724 AC: 110060 AN: 152046 Hom.: 40447 Cov.: 32 AF XY: 0.724 AC XY: 53761 AN XY: 74292

African (AFR) AF: 0.829 AC: 34431 AN: 41516

American (AMR) AF: 0.764 AC: 11657 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4773 AN: 5150

South Asian (SAS) AF: 0.797 AC: 3842 AN: 4820

European-Finnish (FIN) AF: 0.627 AC: 6614 AN: 10548

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43934 AN: 67968

Other (OTH) AF: 0.716 AC: 1513 AN: 2114

Alfa AF: 0.687 Hom.: 4501

Bravo AF: 0.740

Asia WGS AF: 0.869 AC: 3020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs1515104; hg19: chr2-227092405;