12-91067148-C-T

Variant names:

• chr12-91067148-C-T
• rs10859103

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 0.653 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
• Publications: 4 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 = 0.777 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.338 AC: 13984 AN: 41390

American (AMR) AF: 0.700 AC: 10631 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2662 AN: 3464

East Asian (EAS) AF: 0.797 AC: 4074 AN: 5112

South Asian (SAS) AF: 0.738 AC: 3557 AN: 4818

European-Finnish (FIN) AF: 0.827 AC: 8728 AN: 10558

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53124 AN: 67846

Other (OTH) AF: 0.696 AC: 1467 AN: 2108

Alfa AF: 0.740 Hom.: 23294

Bravo AF: 0.627

Asia WGS AF: 0.726 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10859103; hg19: chr12-91460925;