rs197273

Variant names:

• chr2-161038152-A-G
• rs197273

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 0.58 in 151,978 control chromosomes in the GnomAD database, including 26,155 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 0.58 (26155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88073 AN: 151860 Hom.: 26133 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.580 AC: 88141 AN: 151978 Hom.: 26155 Cov.: 32 AF XY: 0.577 AC XY: 42827 AN XY: 74272

African (AFR) AF: 0.684 AC: 28349 AN: 41448

American (AMR) AF: 0.655 AC: 10004 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2365 AN: 5160

South Asian (SAS) AF: 0.611 AC: 2946 AN: 4818

European-Finnish (FIN) AF: 0.462 AC: 4864 AN: 10530

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35940 AN: 67952

Other (OTH) AF: 0.556 AC: 1175 AN: 2114

Alfa AF: 0.551 Hom.: 70298

Bravo AF: 0.600

Asia WGS AF: 0.508 AC: 1768 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs197273; hg19: chr2-161894663;