rs2313543

Variant names:

• chr3-1080685-A-G
• rs2313543

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 0.184 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.186 AC: 7732 AN: 41472

American (AMR) AF: 0.152 AC: 2325 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3466

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5174

South Asian (SAS) AF: 0.0870 AC: 420 AN: 4830

European-Finnish (FIN) AF: 0.133 AC: 1409 AN: 10606

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14657 AN: 67958

Other (OTH) AF: 0.191 AC: 403 AN: 2112

Alfa AF: 0.205 Hom.: 2956

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

Other links and lift over

dbSNP: rs2313543; hg19: chr3-1122369;