rs2313543

Positions:

• chr3-1080685-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 0.184 in 152,082 control chromosomes in the GnomAD database, including 2,711 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 0.18 (2711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 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: 0.185 AC: 28051 AN: 151964 Hom.: 2709 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.184 AC: 28053 AN: 152082 Hom.: 2711 Cov.: 32 AF XY: 0.178 AC XY: 13249 AN XY: 74358

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.191

Alfa AF: 0.204 Hom.: 2493

Bravo AF: 0.188

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2313543; hg19: chr3-1122369;