rs1866813

Variant names:

• chr3-137083096-A-C
• rs1866813

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 0.139 in 151,984 control chromosomes in the GnomAD database, including 1,705 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 0.14 (1705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 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: 0.139 AC: 21058 AN: 151866 Hom.: 1703 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.139 AC: 21073 AN: 151984 Hom.: 1705 Cov.: 32 AF XY: 0.145 AC XY: 10752 AN XY: 74286

African (AFR) AF: 0.101 AC: 4204 AN: 41470

American (AMR) AF: 0.211 AC: 3212 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1253 AN: 5146

South Asian (SAS) AF: 0.180 AC: 865 AN: 4814

European-Finnish (FIN) AF: 0.208 AC: 2197 AN: 10564

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8492 AN: 67956

Other (OTH) AF: 0.131 AC: 277 AN: 2114

Alfa AF: 0.131 Hom.: 654

Bravo AF: 0.140

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.80
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs1866813; hg19: chr3-136801938;