rs2918206

Variant names:

• chr3-115729685-G-A
• rs2918206

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 0.481 in 151,946 control chromosomes in the GnomAD database, including 18,724 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 0.48 (18724 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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: 0.481 AC: 73041 AN: 151828 Hom.: 18688 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.481 AC: 73123 AN: 151946 Hom.: 18724 Cov.: 31 AF XY: 0.481 AC XY: 35735 AN XY: 74270

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.470

Alfa AF: 0.440 Hom.: 2580

Bravo AF: 0.490

Asia WGS AF: 0.323 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2918206; hg19: chr3-115448532;