12-745165-T-C

Variant names:

• chr12-745165-T-C
• rs7137188

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 0.522 in 152,014 control chromosomes in the GnomAD database, including 21,231 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 0.52 (21231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.522 AC: 79340 AN: 151898 Hom.: 21209 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.522 AC: 79403 AN: 152014 Hom.: 21231 Cov.: 32 AF XY: 0.526 AC XY: 39093 AN XY: 74302

African (AFR) AF: 0.624 AC: 25869 AN: 41468

American (AMR) AF: 0.443 AC: 6762 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2055 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1851 AN: 5180

South Asian (SAS) AF: 0.607 AC: 2927 AN: 4824

European-Finnish (FIN) AF: 0.526 AC: 5543 AN: 10542

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32642 AN: 67930

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.493 Hom.: 85135

Bravo AF: 0.519

Asia WGS AF: 0.502 AC: 1748 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.9
DANN	Benign	0.84
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs7137188; hg19: chr12-854331;