rs762802716

Variant names:

• chr1-54088603-C-G
• rs762802716
• NM_153035.3:c.251C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-54088603-C-G
• chr1-54088603-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_153035.3(TCEANC2):​c.251C>G​(p.Thr84Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000138 in 1,447,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T84I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: TCEANC2 NM_153035.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.76

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.32092917).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEANC2	NM_153035.3	c.251C>G	p.Thr84Ser	missense_variant	Exon 4 of 5	ENST00000234827.6	NP_694580.1
TCEANC2	NR_130900.2	n.302C>G		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCEANC2	ENST00000234827.6	c.251C>G	p.Thr84Ser	missense_variant	Exon 4 of 5	1	NM_153035.3	ENSP00000234827.1
TCEANC2	ENST00000371331.1	c.341C>G	p.Thr114Ser	missense_variant	Exon 3 of 4	2		ENSP00000360382.1
TCEANC2	ENST00000498272.1	n.323C>G		non_coding_transcript_exon_variant	Exon 3 of 5	2
TCEANC2	ENST00000648983.1	n.251C>G		non_coding_transcript_exon_variant	Exon 4 of 6			ENSP00000498109.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000138 AC: 2 AN: 1447742 Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1 AN XY: 719840

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000240

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.03e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.039	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.032	T;T
Eigen	Benign	0.14
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.65	T;T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.32	T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	1.6	L;.
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-1.6	N;N
REVEL	Benign	0.096
Sift	Uncertain	0.014	D;D
Sift4G	Uncertain	0.028	D;D
Polyphen		0.39	B;.
Vest4		0.45
MutPred		0.33		Gain of helix (P = 0.0199);.;
MVP		0.040
MPC		0.35
ClinPred		0.83	D
GERP RS		5.9
Varity_R		0.30
gMVP		0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs762802716; hg19: chr1-54554276;