12-69130143-C-T

Variant names:

• chr12-69130143-C-T
• rs10784762

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 0.57 in 152,002 control chromosomes in the GnomAD database, including 24,906 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 0.57 (24906 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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: 0.570 AC: 86552 AN: 151884 Hom.: 24905 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.570 AC: 86578 AN: 152002 Hom.: 24906 Cov.: 33 AF XY: 0.568 AC XY: 42230 AN XY: 74306

African (AFR) AF: 0.497 AC: 20591 AN: 41448

American (AMR) AF: 0.581 AC: 8877 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2036 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3758 AN: 5178

South Asian (SAS) AF: 0.673 AC: 3239 AN: 4812

European-Finnish (FIN) AF: 0.533 AC: 5622 AN: 10556

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.594 AC: 40381 AN: 67948

Other (OTH) AF: 0.586 AC: 1236 AN: 2108

Alfa AF: 0.592 Hom.: 119147

Bravo AF: 0.570

Asia WGS AF: 0.642 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.49
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs10784762; hg19: chr12-69523923;