rs191115

Variant names:

• chr2-125335238-G-A
• rs191115

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 0.482 in 144,116 control chromosomes in the GnomAD database, including 17,726 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 (17726 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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: 0.482 AC: 69409 AN: 144046 Hom.: 17708 Cov.: 23

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.0573

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.482 AC: 69455 AN: 144116 Hom.: 17726 Cov.: 23 AF XY: 0.469 AC XY: 32722 AN XY: 69758

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.0573

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.472

Alfa AF: 0.501 Hom.: 2440

Bravo AF: 0.477

Asia WGS AF: 0.188 AC: 656 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs191115; hg19: chr2-126092815;