rs12692245

Variant names:

• chr2-238747096-G-A
• rs12692245

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 0.573 in 152,140 control chromosomes in the GnomAD database, including 25,018 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 0.57 (25018 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.719 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: 0.573 AC: 87079 AN: 152022 Hom.: 24996 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.573 AC: 87151 AN: 152140 Hom.: 25018 Cov.: 33 AF XY: 0.577 AC XY: 42918 AN XY: 74388

African (AFR) AF: 0.576 AC: 23910 AN: 41494

American (AMR) AF: 0.513 AC: 7847 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1845 AN: 3468

East Asian (EAS) AF: 0.715 AC: 3696 AN: 5170

South Asian (SAS) AF: 0.740 AC: 3569 AN: 4826

European-Finnish (FIN) AF: 0.607 AC: 6431 AN: 10594

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38078 AN: 67976

Other (OTH) AF: 0.560 AC: 1183 AN: 2112

Alfa AF: 0.555 Hom.: 4247

Bravo AF: 0.563

Asia WGS AF: 0.705 AC: 2449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.012
DANN	Benign	0.58
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs12692245; hg19: chr2-239655737;