12-67142879-C-T

Variant names:

• chr12-67142879-C-T
• rs1526832

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.82 in 152,144 control chromosomes in the GnomAD database, including 53,882 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 0.82 (53882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.94 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: 0.821 AC: 124739 AN: 152026 Hom.: 53870 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.820 AC: 124786 AN: 152144 Hom.: 53882 Cov.: 32 AF XY: 0.823 AC XY: 61209 AN XY: 74370

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.841

Alfa AF: 0.913 Hom.: 34968

Bravo AF: 0.803

Asia WGS AF: 0.923 AC: 3210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1526832; hg19: chr12-67536659;