chr2-125335238-G-A

Variant names:

• chr2-125335238-G-A
• rs191115

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 0.482 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.575 AC: 22389 AN: 38908

American (AMR) AF: 0.344 AC: 4867 AN: 14164

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1555 AN: 3436

East Asian (EAS) AF: 0.0573 AC: 284 AN: 4954

South Asian (SAS) AF: 0.247 AC: 1131 AN: 4584

European-Finnish (FIN) AF: 0.451 AC: 3757 AN: 8328

Middle Eastern (MID) AF: 0.447 AC: 118 AN: 264

European-Non Finnish (NFE) AF: 0.510 AC: 33966 AN: 66596

Other (OTH) AF: 0.472 AC: 939 AN: 1988

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
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs191115; hg19: chr2-126092815;