rs3181098

Variant names:

• chr2-203705655-G-A
• rs3181098

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 0.345 in 151,938 control chromosomes in the GnomAD database, including 9,204 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 0.34 (9204 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 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: 0.345 AC: 52383 AN: 151820 Hom.: 9205 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.345 AC: 52389 AN: 151938 Hom.: 9204 Cov.: 31 AF XY: 0.346 AC XY: 25685 AN XY: 74250

African (AFR) AF: 0.322 AC: 13373 AN: 41470

American (AMR) AF: 0.324 AC: 4956 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1446 AN: 5162

South Asian (SAS) AF: 0.604 AC: 2909 AN: 4818

European-Finnish (FIN) AF: 0.337 AC: 3544 AN: 10522

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23791 AN: 67912

Other (OTH) AF: 0.338 AC: 712 AN: 2104

Alfa AF: 0.348 Hom.: 1481

Bravo AF: 0.338

Asia WGS AF: 0.449 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3181098; hg19: chr2-204570378;