12-131593637-T-C

Variant names:

• chr12-131593637-T-C
• rs10082970

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 0.764 in 152,120 control chromosomes in the GnomAD database, including 44,794 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 0.76 (44794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.823 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: 0.764 AC: 116184 AN: 152002 Hom.: 44788 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.764 AC: 116231 AN: 152120 Hom.: 44794 Cov.: 32 AF XY: 0.755 AC XY: 56176 AN XY: 74366

African (AFR) AF: 0.705 AC: 29257 AN: 41494

American (AMR) AF: 0.835 AC: 12772 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3025 AN: 3472

East Asian (EAS) AF: 0.711 AC: 3674 AN: 5166

South Asian (SAS) AF: 0.605 AC: 2914 AN: 4814

European-Finnish (FIN) AF: 0.647 AC: 6843 AN: 10580

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.810 AC: 55066 AN: 67978

Other (OTH) AF: 0.791 AC: 1673 AN: 2116

Alfa AF: 0.800 Hom.: 79889

Bravo AF: 0.782

Asia WGS AF: 0.653 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10082970;

hg19: chr12-132078182;