chr2-225386225-G-A

Variant names:

• chr2-225386225-G-A
• rs1517492

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 0.781 in 152,192 control chromosomes in the GnomAD database, including 46,763 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 0.78 (46763 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 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: 0.781 AC: 118746 AN: 152074 Hom.: 46724 Cov.: 33

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.781 AC: 118831 AN: 152192 Hom.: 46763 Cov.: 33 AF XY: 0.779 AC XY: 57927 AN XY: 74402

African (AFR) AF: 0.829 AC: 34465 AN: 41552

American (AMR) AF: 0.749 AC: 11439 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2615 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2860 AN: 4818

European-Finnish (FIN) AF: 0.806 AC: 8536 AN: 10594

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53705 AN: 67988

Other (OTH) AF: 0.776 AC: 1642 AN: 2116

Alfa AF: 0.768 Hom.: 4278

Bravo AF: 0.798

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1517492; hg19: chr2-226250941;