chr12-63384174-C-T

Variant names:

• chr12-63384174-C-T
• rs722919

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 0.154 in 151,892 control chromosomes in the GnomAD database, including 2,163 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 0.15 (2163 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 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: 0.154 AC: 23342 AN: 151774 Hom.: 2151 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0445

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.154 AC: 23396 AN: 151892 Hom.: 2163 Cov.: 31 AF XY: 0.160 AC XY: 11838 AN XY: 74218

African (AFR) AF: 0.194 AC: 8040 AN: 41404

American (AMR) AF: 0.187 AC: 2858 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0445 AC: 154 AN: 3462

East Asian (EAS) AF: 0.440 AC: 2257 AN: 5126

South Asian (SAS) AF: 0.204 AC: 981 AN: 4808

European-Finnish (FIN) AF: 0.142 AC: 1495 AN: 10552

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7193 AN: 67980

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.119 Hom.: 5552

Bravo AF: 0.158

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.36
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs722919; hg19: chr12-63777954;