12-91079228-T-C

Variant names:

• chr12-91079228-T-C
• rs10859105

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 0.587 in 151,348 control chromosomes in the GnomAD database, including 28,639 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 0.59 (28639 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.587 AC: 88737 AN: 151230 Hom.: 28629 Cov.: 30

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.587 AC: 88767 AN: 151348 Hom.: 28639 Cov.: 30 AF XY: 0.594 AC XY: 43916 AN XY: 73922

African (AFR) AF: 0.309 AC: 12800 AN: 41366

American (AMR) AF: 0.670 AC: 10156 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2266 AN: 3456

East Asian (EAS) AF: 0.676 AC: 3476 AN: 5140

South Asian (SAS) AF: 0.777 AC: 3718 AN: 4784

European-Finnish (FIN) AF: 0.778 AC: 8122 AN: 10438

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.683 AC: 46220 AN: 67716

Other (OTH) AF: 0.611 AC: 1282 AN: 2098

Alfa AF: 0.682 Hom.: 18107

Bravo AF: 0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10859105; hg19: chr12-91473005;