2-159913520-G-A

Variant names:

• chr2-159913520-G-A
• rs12692575

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 0.714 in 152,096 control chromosomes in the GnomAD database, including 39,745 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 0.71 (39745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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: 0.714 AC: 108489 AN: 151978 Hom.: 39711 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.714 AC: 108579 AN: 152096 Hom.: 39745 Cov.: 32 AF XY: 0.713 AC XY: 53043 AN XY: 74360

African (AFR) AF: 0.549 AC: 22742 AN: 41434

American (AMR) AF: 0.771 AC: 11786 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2418 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4212 AN: 5176

South Asian (SAS) AF: 0.592 AC: 2853 AN: 4818

European-Finnish (FIN) AF: 0.808 AC: 8554 AN: 10590

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53563 AN: 68000

Other (OTH) AF: 0.719 AC: 1518 AN: 2112

Alfa AF: 0.763 Hom.: 189115

Bravo AF: 0.709

Asia WGS AF: 0.708 AC: 2465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.49
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs12692575; hg19: chr2-160770031;