12-121040109-T-C

Variant names:

• chr12-121040109-T-C
• rs4556628

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 0.713 in 151,882 control chromosomes in the GnomAD database, including 39,002 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 0.71 (39002 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.713 AC: 108279 AN: 151766 Hom.: 38969 Cov.: 30

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.779

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.713 AC: 108359 AN: 151882 Hom.: 39002 Cov.: 30 AF XY: 0.715 AC XY: 53087 AN XY: 74208

African (AFR) AF: 0.666 AC: 27579 AN: 41400

American (AMR) AF: 0.802 AC: 12230 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2543 AN: 3464

East Asian (EAS) AF: 0.888 AC: 4566 AN: 5140

South Asian (SAS) AF: 0.887 AC: 4277 AN: 4820

European-Finnish (FIN) AF: 0.631 AC: 6661 AN: 10552

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.707 AC: 48048 AN: 67950

Other (OTH) AF: 0.740 AC: 1555 AN: 2102

Alfa AF: 0.711 Hom.: 79707

Bravo AF: 0.721

Asia WGS AF: 0.883 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4556628; hg19: chr12-121477912;