rs12046178

Variant names:

• chr1-54106502-T-C
• rs12046178
• ENST00000498272.1:n.1071-4550T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000498272.1(TCEANC2):​n.1071-4550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,082 control chromosomes in the GnomAD database, including 7,607 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 0.31 (7607 hom., cov: 33)
• Consequence: TCEANC2 ENST00000498272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 2 publications found

Genes affected

TCEANC2 (HGNC:26494): (transcription elongation factor A N-terminal and central domain containing 2) Predicted to be involved in transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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 (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498272.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCEANC2	NR_130900.2		n.1050-4550T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCEANC2	ENST00000498272.1	TSL:2	n.1071-4550T>C		intron	N/A
	TCEANC2	ENST00000648983.1		n.*372-4550T>C		intron	N/A	ENSP00000498109.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46809 AN: 151966 Hom.: 7601 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.308 AC: 46821 AN: 152082 Hom.: 7607 Cov.: 33 AF XY: 0.305 AC XY: 22653 AN XY: 74334

African (AFR) AF: 0.229 AC: 9495 AN: 41490

American (AMR) AF: 0.439 AC: 6708 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3468

East Asian (EAS) AF: 0.364 AC: 1886 AN: 5176

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2488 AN: 10574

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22702 AN: 67962

Other (OTH) AF: 0.370 AC: 780 AN: 2110

Alfa AF: 0.310 Hom.: 979

Bravo AF: 0.326

Asia WGS AF: 0.289 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.84
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12046178; hg19: chr1-54572175;