2-102403459-A-G

Variant names:

• chr2-102403459-A-G
• rs1035127

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 0.773 in 151,862 control chromosomes in the GnomAD database, including 46,300 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 0.77 (46300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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: 0.773 AC: 117226 AN: 151746 Hom.: 46257 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.773 AC: 117318 AN: 151862 Hom.: 46300 Cov.: 32 AF XY: 0.766 AC XY: 56880 AN XY: 74236

African (AFR) AF: 0.888 AC: 36860 AN: 41492

American (AMR) AF: 0.603 AC: 9208 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2659 AN: 3466

East Asian (EAS) AF: 0.551 AC: 2844 AN: 5166

South Asian (SAS) AF: 0.546 AC: 2630 AN: 4820

European-Finnish (FIN) AF: 0.812 AC: 8596 AN: 10588

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52084 AN: 67762

Other (OTH) AF: 0.759 AC: 1601 AN: 2108

Alfa AF: 0.697 Hom.: 8061

Bravo AF: 0.762

Asia WGS AF: 0.579 AC: 2009 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.43
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1035127; hg19: chr2-103019919;