2-315215-A-G

Variant names:

• chr2-315215-A-G
• rs4643574

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.875 in 152,294 control chromosomes in the GnomAD database, including 58,759 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 0.87 (58759 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 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: 0.875 AC: 133143 AN: 152176 Hom.: 58727 Cov.: 35

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.875 AC: 133232 AN: 152294 Hom.: 58759 Cov.: 35 AF XY: 0.873 AC XY: 65011 AN XY: 74470

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.873

Alfa AF: 0.893 Hom.: 93294

Bravo AF: 0.870

Asia WGS AF: 0.743 AC: 2586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4643574; hg19: chr2-315215;