chr12-128153529-G-A

Variant names:

• chr12-128153529-G-A
• rs997269

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 0.431 in 151,912 control chromosomes in the GnomAD database, including 14,321 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 0.43 (14321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.431 AC: 65486 AN: 151794 Hom.: 14313 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.431 AC: 65541 AN: 151912 Hom.: 14321 Cov.: 32 AF XY: 0.438 AC XY: 32528 AN XY: 74236

African (AFR) AF: 0.373 AC: 15453 AN: 41420

American (AMR) AF: 0.460 AC: 7014 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1520 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2765 AN: 5138

South Asian (SAS) AF: 0.528 AC: 2542 AN: 4810

European-Finnish (FIN) AF: 0.533 AC: 5628 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29122 AN: 67954

Other (OTH) AF: 0.445 AC: 937 AN: 2106

Alfa AF: 0.434 Hom.: 7568

Bravo AF: 0.425

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.27
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs997269; hg19: chr12-128638074;