chr12-63044892-C-T

Variant names:

• chr12-63044892-C-T
• rs12815621

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 0.113 in 152,018 control chromosomes in the GnomAD database, including 1,083 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 0.11 (1083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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: 0.113 AC: 17182 AN: 151900 Hom.: 1079 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0922

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00387

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.113 AC: 17209 AN: 152018 Hom.: 1083 Cov.: 31 AF XY: 0.115 AC XY: 8567 AN XY: 74308

African (AFR) AF: 0.102 AC: 4227 AN: 41482

American (AMR) AF: 0.0920 AC: 1406 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3470

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5160

South Asian (SAS) AF: 0.0802 AC: 386 AN: 4812

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10550

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8543 AN: 67956

Other (OTH) AF: 0.102 AC: 214 AN: 2108

Alfa AF: 0.122 Hom.: 1278

Bravo AF: 0.105

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.19
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs12815621; hg19: chr12-63438672;