chr12-53239847-A-T

Variant names:

• chr12-53239847-A-T
• rs10783561

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 0.6 in 151,760 control chromosomes in the GnomAD database, including 27,816 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 0.60 (27816 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.781 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: 0.600 AC: 91034 AN: 151640 Hom.: 27780 Cov.: 30

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.600 AC: 91128 AN: 151760 Hom.: 27816 Cov.: 30 AF XY: 0.602 AC XY: 44632 AN XY: 74130

African (AFR) AF: 0.650 AC: 26870 AN: 41350

American (AMR) AF: 0.615 AC: 9387 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3468

East Asian (EAS) AF: 0.802 AC: 4133 AN: 5156

South Asian (SAS) AF: 0.748 AC: 3607 AN: 4820

European-Finnish (FIN) AF: 0.531 AC: 5567 AN: 10488

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37781 AN: 67908

Other (OTH) AF: 0.605 AC: 1273 AN: 2104

Alfa AF: 0.571 Hom.: 2949

Bravo AF: 0.609

Asia WGS AF: 0.734 AC: 2552 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	0.037
DANN	Benign	0.31
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs10783561; hg19: chr12-53633631; COSMIC: COSV62998542;