12-63056902-A-G

Variant names:

• chr12-63056902-A-G
• rs3913039

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 0.354 in 151,888 control chromosomes in the GnomAD database, including 9,803 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 0.35 (9803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.427 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: 0.354 AC: 53740 AN: 151768 Hom.: 9800 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.354 AC: 53750 AN: 151888 Hom.: 9803 Cov.: 31 AF XY: 0.357 AC XY: 26492 AN XY: 74216

African (AFR) AF: 0.259 AC: 10711 AN: 41420

American (AMR) AF: 0.404 AC: 6163 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1462 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1204 AN: 5150

South Asian (SAS) AF: 0.443 AC: 2132 AN: 4818

European-Finnish (FIN) AF: 0.389 AC: 4098 AN: 10530

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26876 AN: 67922

Other (OTH) AF: 0.365 AC: 768 AN: 2104

Alfa AF: 0.387 Hom.: 19675

Bravo AF: 0.350

Asia WGS AF: 0.357 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs3913039; hg19: chr12-63450682;