12-90382160-C-T

Variant names:

• chr12-90382160-C-T
• rs811

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 0.739 in 152,066 control chromosomes in the GnomAD database, including 42,832 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 0.74 (42832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.739 AC: 112281 AN: 151950 Hom.: 42775 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.739 AC: 112397 AN: 152066 Hom.: 42832 Cov.: 32 AF XY: 0.736 AC XY: 54724 AN XY: 74308

African (AFR) AF: 0.934 AC: 38760 AN: 41518

American (AMR) AF: 0.728 AC: 11136 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2049 AN: 3468

East Asian (EAS) AF: 0.802 AC: 4142 AN: 5166

South Asian (SAS) AF: 0.717 AC: 3447 AN: 4808

European-Finnish (FIN) AF: 0.604 AC: 6365 AN: 10542

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44107 AN: 67954

Other (OTH) AF: 0.717 AC: 1514 AN: 2112

Alfa AF: 0.589 Hom.: 1617

Bravo AF: 0.753

Asia WGS AF: 0.801 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.20
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs811; hg19: chr12-90775937;