12-91075283-G-C

Variant names:

• chr12-91075283-G-C
• rs10745551

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 0.561 in 151,826 control chromosomes in the GnomAD database, including 25,777 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 0.56 (25777 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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: 0.561 AC: 85079 AN: 151708 Hom.: 25771 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.561 AC: 85120 AN: 151826 Hom.: 25777 Cov.: 30 AF XY: 0.565 AC XY: 41889 AN XY: 74198

African (AFR) AF: 0.313 AC: 12945 AN: 41394

American (AMR) AF: 0.567 AC: 8648 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2282 AN: 3472

East Asian (EAS) AF: 0.645 AC: 3317 AN: 5142

South Asian (SAS) AF: 0.638 AC: 3067 AN: 4810

European-Finnish (FIN) AF: 0.735 AC: 7747 AN: 10544

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45172 AN: 67910

Other (OTH) AF: 0.573 AC: 1209 AN: 2110

Alfa AF: 0.598 Hom.: 3543

Bravo AF: 0.536

Asia WGS AF: 0.599 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.35
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10745551; hg19: chr12-91469060;