chr12-63396056-T-G

Variant names:

• chr12-63396056-T-G
• rs1922117

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 0.413 in 151,826 control chromosomes in the GnomAD database, including 13,831 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 0.41 (13831 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.413 AC: 62702 AN: 151708 Hom.: 13807 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.413 AC: 62771 AN: 151826 Hom.: 13831 Cov.: 31 AF XY: 0.418 AC XY: 30987 AN XY: 74190

African (AFR) AF: 0.571 AC: 23629 AN: 41372

American (AMR) AF: 0.383 AC: 5848 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3470

East Asian (EAS) AF: 0.581 AC: 2982 AN: 5132

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4814

European-Finnish (FIN) AF: 0.374 AC: 3933 AN: 10530

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21931 AN: 67930

Other (OTH) AF: 0.386 AC: 811 AN: 2102

Alfa AF: 0.348 Hom.: 37957

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.48
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1922117; hg19: chr12-63789836;