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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRD-GTC2-9	unassigned_transcript_2098	c.-44G>A		upstream_gene_variant

Ensembl

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

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 v4.3

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

Other links and lift over

dbSNP: rs10846771; hg19: chr12-125412006;