chr1-54106570-C-A

Variant names:

• chr1-54106570-C-A
• rs10788972
• ENST00000498272.1:n.1071-4482C>A

Variant summary

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

The ENST00000498272.1(TCEANC2):​n.1071-4482C>A variant causes a intron 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 ENST00000498272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 13 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=-0.99).
• 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 rank	MANE	Protein	UniProt
TCEANC2	NR_130900.2	n.1050-4482C>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCEANC2	ENST00000498272.1	n.1071-4482C>A		intron_variant	Intron 4 of 4	2
TCEANC2	ENST00000648983.1	n.*372-4482C>A		intron_variant	Intron 5 of 5			ENSP00000498109.1

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

African (AFR) AF: 0.836 AC: 34661 AN: 41476

American (AMR) AF: 0.591 AC: 9025 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3472

East Asian (EAS) AF: 0.611 AC: 3155 AN: 5166

South Asian (SAS) AF: 0.372 AC: 1788 AN: 4812

European-Finnish (FIN) AF: 0.331 AC: 3489 AN: 10534

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29484 AN: 67926

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.478 Hom.: 16249

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10788972; hg19: chr1-54572243;