rs3181097

Variant names:

• chr2-203705416-G-A
• rs3181097

Your query was ambiguous. Multiple possible variants found:

• chr2-203705416-G-A
• chr2-203705416-G-T

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 0.103 in 152,096 control chromosomes in the GnomAD database, including 1,405 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 (1405 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.103 AC: 15618 AN: 151978 Hom.: 1399 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.103 AC: 15663 AN: 152096 Hom.: 1405 Cov.: 31 AF XY: 0.106 AC XY: 7847 AN XY: 74356

African (AFR) AF: 0.175 AC: 7266 AN: 41448

American (AMR) AF: 0.110 AC: 1682 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0276 AC: 96 AN: 3472

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5164

South Asian (SAS) AF: 0.0961 AC: 463 AN: 4818

European-Finnish (FIN) AF: 0.0588 AC: 622 AN: 10580

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0430 AC: 2923 AN: 68002

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0647 Hom.: 629

Bravo AF: 0.114

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.71
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs3181097; hg19: chr2-204570139;