rs10788972

chr1-54106570-C-A

Variant summary

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

The ENST00000648983.1(TCEANC2):c.*372-4482C>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,980 control chromosomes in the GnomAD database, including 26,599 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 0.56 (26599 hom., cov: 32)
• Consequence: TCEANC2 ENST00000648983.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCEANC2	NR_130900.2	n.1050-4482C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCEANC2	ENST00000648983.1	c.*372-4482C>A		intron_variant, NMD_transcript_variant
TCEANC2	ENST00000498272.1	n.1071-4482C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85240 AN: 151862 Hom.: 26544 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.562 AC: 85351 AN: 151980 Hom.: 26599 Cov.: 32 AF XY: 0.557 AC XY: 41367 AN XY: 74274

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.596

Alfa AF: 0.468 Hom.: 12685

Bravo AF: 0.599

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.86
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788972; hg19: chr1-54572243;