12-91067889-C-T

Variant names:

• chr12-91067889-C-T
• rs10859104

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 0.227 in 151,878 control chromosomes in the GnomAD database, including 6,101 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 0.23 (6101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.227 AC: 34428 AN: 151760 Hom.: 6075 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.227 AC: 34500 AN: 151878 Hom.: 6101 Cov.: 32 AF XY: 0.218 AC XY: 16222 AN XY: 74248

African (AFR) AF: 0.496 AC: 20529 AN: 41362

American (AMR) AF: 0.160 AC: 2432 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3468

East Asian (EAS) AF: 0.0740 AC: 382 AN: 5160

South Asian (SAS) AF: 0.0568 AC: 274 AN: 4822

European-Finnish (FIN) AF: 0.0817 AC: 867 AN: 10608

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8805 AN: 67928

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.149 Hom.: 3796

Bravo AF: 0.248

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.62
DANN	Benign	0.11
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10859104; hg19: chr12-91461666;