2-176098230-G-A

Variant names:

• chr2-176098230-G-A
• rs847154

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 0.39 in 152,118 control chromosomes in the GnomAD database, including 12,945 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 0.39 (12945 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59281 AN: 152000 Hom.: 12913 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.390 AC: 59365 AN: 152118 Hom.: 12945 Cov.: 33 AF XY: 0.382 AC XY: 28437 AN XY: 74370

African (AFR) AF: 0.580 AC: 24071 AN: 41486

American (AMR) AF: 0.386 AC: 5911 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3468

East Asian (EAS) AF: 0.0645 AC: 333 AN: 5160

South Asian (SAS) AF: 0.239 AC: 1155 AN: 4826

European-Finnish (FIN) AF: 0.295 AC: 3126 AN: 10588

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22717 AN: 67974

Other (OTH) AF: 0.367 AC: 776 AN: 2114

Alfa AF: 0.400 Hom.: 1914

Bravo AF: 0.408

Asia WGS AF: 0.214 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.40
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs847154; hg19: chr2-176962958;