12-128749585-T-A

Variant names:

• chr12-128749585-T-A
• rs7955663

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 0.575 in 152,022 control chromosomes in the GnomAD database, including 25,916 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 0.58 (25916 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.575 AC: 87418 AN: 151904 Hom.: 25896 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.575 AC: 87479 AN: 152022 Hom.: 25916 Cov.: 33 AF XY: 0.570 AC XY: 42382 AN XY: 74298

African (AFR) AF: 0.713 AC: 29549 AN: 41460

American (AMR) AF: 0.425 AC: 6490 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1745 AN: 3464

East Asian (EAS) AF: 0.593 AC: 3068 AN: 5174

South Asian (SAS) AF: 0.549 AC: 2643 AN: 4818

European-Finnish (FIN) AF: 0.532 AC: 5614 AN: 10552

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36436 AN: 67962

Other (OTH) AF: 0.586 AC: 1238 AN: 2114

Alfa AF: 0.564 Hom.: 3068

Bravo AF: 0.574

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.38
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7955663; hg19: chr12-129234130;