chr3-103631596-A-G

Variant names:

• chr3-103631596-A-G
• rs2895256

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 0.062 in 152,120 control chromosomes in the GnomAD database, including 803 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 0.062 (803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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: 0.0618 AC: 9399 AN: 152002 Hom.: 789 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0620 AC: 9425 AN: 152120 Hom.: 803 Cov.: 32 AF XY: 0.0709 AC XY: 5270 AN XY: 74352

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0768

Gnomad4 NFE AF: 0.0173

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0496 Hom.: 96

Bravo AF: 0.0641

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2895256; hg19: chr3-103350440;