12-124927460-C-T

Variant names:

• chr12-124927460-C-T
• rs10846771
• unassigned_transcript_2098:c.-44G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000000000(TRD-GTC2-9):​c.-44G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,160 control chromosomes in the GnomAD database, including 40,544 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 0.72 (40544 hom., cov: 34)
• Consequence: TRD-GTC2-9 ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 8 publications found

Genes affected

TRD-GTC2-9 (HGNC:34911):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 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: 0.718 AC: 109180 AN: 152042 Hom.: 40523 Cov.: 34

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.718 AC: 109247 AN: 152160 Hom.: 40544 Cov.: 34 AF XY: 0.708 AC XY: 52644 AN XY: 74380

African (AFR) AF: 0.698 AC: 28971 AN: 41506

American (AMR) AF: 0.641 AC: 9801 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3040 AN: 3470

East Asian (EAS) AF: 0.146 AC: 757 AN: 5176

South Asian (SAS) AF: 0.780 AC: 3760 AN: 4822

European-Finnish (FIN) AF: 0.642 AC: 6797 AN: 10582

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53580 AN: 68008

Other (OTH) AF: 0.736 AC: 1551 AN: 2108

Alfa AF: 0.765 Hom.: 166342

Bravo AF: 0.711

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	0.036
DANN	Benign	0.50
PhyloP100		-2.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10846771;

hg19: chr12-125412006;