1-54088759-A-G

Variant names:

• chr1-54088759-A-G
• NM_153035.3:c.407A>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_153035.3(TCEANC2):​c.407A>G​(p.Gln136Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,446,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: TCEANC2 NM_153035.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.776

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.024089247).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEANC2	NM_153035.3	c.407A>G	p.Gln136Arg	missense_variant	Exon 4 of 5	ENST00000234827.6	NP_694580.1
TCEANC2	NR_130900.2	n.458A>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.407A>G	p.Gln136Arg	missense_variant	Exon 4 of 5	1	NM_153035.3	ENSP00000234827.1
TCEANC2	ENST00000371331.1	c.497A>G	p.Gln166Arg	missense_variant	Exon 3 of 4	2		ENSP00000360382.1
TCEANC2	ENST00000498272.1	n.479A>G		non_coding_transcript_exon_variant	Exon 3 of 5	2
TCEANC2	ENST00000648983.1	n.407A>G		non_coding_transcript_exon_variant	Exon 4 of 6			ENSP00000498109.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.91e-7 AC: 1 AN: 1446754 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 718026

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.06e-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	0.070
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.7
DANN	Benign	0.55
DEOGEN2	Benign	0.0034	T;T
Eigen	Benign	-1.2
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.67	T;T
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.024	T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-0.59	N;.
PrimateAI	Benign	0.29	T
PROVEAN	Benign	1.8	N;N
REVEL	Benign	0.034
Sift	Benign	1.0	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;.
Vest4		0.081
MutPred		0.21		Gain of MoRF binding (P = 0.0136);.;
MVP		0.014
MPC		0.20
ClinPred		0.12	T
GERP RS		-0.17
Varity_R		0.024
gMVP		0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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.

Other links and lift over

hg19: chr1-54554432;