chr12-128749585-T-A

Variant names:

• chr12-128749585-T-A
• rs7955663

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.586

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7955663; hg19: chr12-129234130;