rs12046178

chr1-54106502-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648983.1(TCEANC2):c.*372-4550T>C variant causes a intron, NMD transcript 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 ENST00000648983.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCEANC2	NR_130900.2	n.1050-4550T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCEANC2	ENST00000648983.1	c.*372-4550T>C		intron_variant, NMD_transcript_variant
TCEANC2	ENST00000498272.1	n.1071-4550T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.370

Alfa AF: 0.313 Hom.: 963

Bravo AF: 0.326

Asia WGS AF: 0.289 AC: 1008 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	8.6
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12046178; hg19: chr1-54572175;