2-75313470-A-G

Variant names:

• chr2-75313470-A-G
• rs10515919

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 0.211 in 152,086 control chromosomes in the GnomAD database, including 3,738 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 0.21 (3738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.864

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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: 0.211 AC: 32110 AN: 151968 Hom.: 3735 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.211 AC: 32141 AN: 152086 Hom.: 3738 Cov.: 32 AF XY: 0.216 AC XY: 16064 AN XY: 74336

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.187

Alfa AF: 0.189 Hom.: 1608

Bravo AF: 0.213

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515919; hg19: chr2-75540596;