chr3-102484201-C-A

Position:

• chr3-102484201-C-A

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 0.101 in 152,218 control chromosomes in the GnomAD database, including 1,114 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 0.10 (1114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15304 AN: 152098 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.101 AC: 15318 AN: 152218 Hom.: 1114 Cov.: 32 AF XY: 0.104 AC XY: 7726 AN XY: 74404

Gnomad4 AFR AF: 0.0434

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0976

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0990 Hom.: 1031

Bravo AF: 0.105

Asia WGS AF: 0.170 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2063640; hg19: chr3-102203045;