chr2-103638106-A-G

Variant names:

• chr2-103638106-A-G
• rs264963

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 0.499 in 151,752 control chromosomes in the GnomAD database, including 19,570 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 0.50 (19570 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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: 0.499 AC: 75607 AN: 151634 Hom.: 19538 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.499 AC: 75678 AN: 151752 Hom.: 19570 Cov.: 31 AF XY: 0.504 AC XY: 37381 AN XY: 74154

African (AFR) AF: 0.423 AC: 17524 AN: 41390

American (AMR) AF: 0.559 AC: 8517 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3464

East Asian (EAS) AF: 0.931 AC: 4744 AN: 5096

South Asian (SAS) AF: 0.712 AC: 3426 AN: 4810

European-Finnish (FIN) AF: 0.491 AC: 5178 AN: 10546

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32879 AN: 67896

Other (OTH) AF: 0.495 AC: 1047 AN: 2114

Alfa AF: 0.496 Hom.: 71282

Bravo AF: 0.501

Asia WGS AF: 0.803 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs264963; hg19: chr2-104254564;