chr12-90962263-T-G

Variant names:

• chr12-90962263-T-G
• rs12820238

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 0.718 in 152,034 control chromosomes in the GnomAD database, including 41,226 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 0.72 (41226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109135 AN: 151916 Hom.: 41223 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.718 AC: 109160 AN: 152034 Hom.: 41226 Cov.: 31 AF XY: 0.720 AC XY: 53527 AN XY: 74336

African (AFR) AF: 0.459 AC: 19020 AN: 41432

American (AMR) AF: 0.759 AC: 11598 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2869 AN: 3468

East Asian (EAS) AF: 0.802 AC: 4142 AN: 5164

South Asian (SAS) AF: 0.722 AC: 3478 AN: 4814

European-Finnish (FIN) AF: 0.857 AC: 9075 AN: 10586

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.832 AC: 56537 AN: 67966

Other (OTH) AF: 0.750 AC: 1588 AN: 2116

Alfa AF: 0.724 Hom.: 4438

Bravo AF: 0.698

Asia WGS AF: 0.725 AC: 2521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.68
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12820238; hg19: chr12-91356040;