Variant chr1-54054445-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_153035.3(TCEANC2):c.23C>A(p.Thr8Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

TCEANC2
NM_153035.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.55

Variant links:

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]

TCEANC2 links:

TCEANC2 (HGNC:):

TCEANC2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.13409108).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCEANC2	NM_153035.3 linkuse as main transcript	c.23C>A	p.Thr8Lys	missense_variant	2/5	ENST00000234827.6	NP_694580.1	Q96MN5-1
TCEANC2	NR_130900.2 linkuse as main transcript	n.216C>A		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TCEANC2	ENST00000234827.6 linkuse as main transcript	c.23C>A	p.Thr8Lys	missense_variant	2/5	1	NM_153035.3	ENSP00000234827.1	Q96MN5-1
TCEANC2	ENST00000371331.1 linkuse as main transcript	c.113C>A	p.Thr38Lys	missense_variant	1/4	2		ENSP00000360382.1	X6R7X0
TCEANC2	ENST00000498272.1 linkuse as main transcript	n.237C>A		non_coding_transcript_exon_variant	2/5	2
TCEANC2	ENST00000648983.1 linkuse as main transcript	n.23C>A		non_coding_transcript_exon_variant	2/6			ENSP00000498109.1	Q96MN5-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461842

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 06, 2024

The c.23C>A (p.T8K) alteration is located in exon 2 (coding exon 1) of the TCEANC2 gene. This alteration results from a C to A substitution at nucleotide position 23, causing the threonine (T) at amino acid position 8 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.16

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.83

DEOGEN2

Benign

0.015

T;T

Eigen

Benign

-0.13

Eigen_PC

Benign

0.11

FATHMM_MKL

Benign

0.67

LIST_S2

Benign

0.60

T;T

M_CAP

Benign

0.0013

MetaRNN

Benign

0.13

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.82

L;.

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-0.60

N;N

REVEL

Benign

0.049

Sift

Benign

0.20

T;T

Sift4G

Benign

0.27

T;T

Polyphen

0.0

B;.

Vest4

0.24

MutPred

0.39

Gain of methylation at T8 (P = 0.0124);.;

MVP

0.088

MPC

0.23

ClinPred

0.83

GERP RS

5.1

Varity_R

0.15

gMVP

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over