12-91067148-C-T

Variant names:

• chr12-91067148-C-T
• rs10859103

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 0.653 in 151,678 control chromosomes in the GnomAD database, including 35,285 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 0.65 (35285 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

ACMG classification

Verdict is Benign. Variant got -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 = 0.777 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: 0.653 AC: 99029 AN: 151560 Hom.: 35280 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.653 AC: 99052 AN: 151678 Hom.: 35285 Cov.: 31 AF XY: 0.659 AC XY: 48803 AN XY: 74112

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.696

Alfa AF: 0.742 Hom.: 20974

Bravo AF: 0.627

Asia WGS AF: 0.726 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10859103; hg19: chr12-91460925;