chr3-103631596-A-G

Position:

• chr3-103631596-A-G

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.103631596A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;