2-191160178-A-G

Variant names:

• chr2-191160178-A-G
• rs13001658

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 0.63 in 152,072 control chromosomes in the GnomAD database, including 31,301 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 0.63 (31301 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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 (SAS) allele frequency at 95% confidence interval = 0.724 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: 0.630 AC: 95749 AN: 151954 Hom.: 31285 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.630 AC: 95816 AN: 152072 Hom.: 31301 Cov.: 33 AF XY: 0.635 AC XY: 47181 AN XY: 74316

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.623

Alfa AF: 0.693 Hom.: 60195

Bravo AF: 0.620

Asia WGS AF: 0.645 AC: 2239 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	4.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13001658; hg19: chr2-192024904;