12-126787123-C-T

Variant names:

• chr12-126787123-C-T
• rs4765114

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 0.807 in 152,206 control chromosomes in the GnomAD database, including 52,566 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 0.81 (52566 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.807 AC: 122806 AN: 152088 Hom.: 52543 Cov.: 33

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.807 AC: 122865 AN: 152206 Hom.: 52566 Cov.: 33 AF XY: 0.815 AC XY: 60643 AN XY: 74428

African (AFR) AF: 0.494 AC: 20482 AN: 41468

American (AMR) AF: 0.890 AC: 13628 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2963 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5164 AN: 5166

South Asian (SAS) AF: 0.922 AC: 4457 AN: 4832

European-Finnish (FIN) AF: 0.968 AC: 10274 AN: 10616

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 63021 AN: 68028

Other (OTH) AF: 0.844 AC: 1784 AN: 2114

Alfa AF: 0.892 Hom.: 36135

Bravo AF: 0.787

Asia WGS AF: 0.931 AC: 3236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4765114; hg19: chr12-127271669;