2-60443342-A-G

Variant names:

• chr2-60443342-A-G
• rs12468946

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 0.513 in 152,056 control chromosomes in the GnomAD database, including 20,446 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 0.51 (20446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.513 AC: 77880 AN: 151938 Hom.: 20416 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.513 AC: 77959 AN: 152056 Hom.: 20446 Cov.: 32 AF XY: 0.515 AC XY: 38281 AN XY: 74342

African (AFR) AF: 0.546 AC: 22652 AN: 41464

American (AMR) AF: 0.543 AC: 8286 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3960 AN: 5172

South Asian (SAS) AF: 0.505 AC: 2434 AN: 4818

European-Finnish (FIN) AF: 0.544 AC: 5755 AN: 10576

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32290 AN: 67972

Other (OTH) AF: 0.460 AC: 973 AN: 2116

Alfa AF: 0.490 Hom.: 69334

Bravo AF: 0.518

Asia WGS AF: 0.612 AC: 2125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs12468946; hg19: chr2-60670477;