chrX-80442996-A-T

Variant names:

• chrX-80442996-A-T
• rs1008391005
• NM_152630.5:c.457A>T

Variant summary

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

The NM_152630.5(TENT5D):​c.457A>T​(p.Thr153Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,097,764 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 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: 23)
  • Exomes 𝑓: 9.1e-7 (0 hom. 0 hem.)
• Consequence: TENT5D NM_152630.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.24

Genes affected

TENT5D (HGNC:28399): (terminal nucleotidyltransferase 5D) Antibodies against the protein encoded by this gene were found only in plasma from cancer patients. While it may be a target for immunotherapy, the function of this gene is unknown. [provided by RefSeq, Dec 2009]

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=0.06412685).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT5D	NM_152630.5	c.457A>T	p.Thr153Ser	missense_variant	Exon 3 of 3	ENST00000308293.6	NP_689843.1
TENT5D	NM_001170574.2	c.457A>T	p.Thr153Ser	missense_variant	Exon 5 of 5		NP_001164045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5D	ENST00000308293.6	c.457A>T	p.Thr153Ser	missense_variant	Exon 3 of 3	1	NM_152630.5	ENSP00000308575.5
TENT5D	ENST00000538312.5	c.457A>T	p.Thr153Ser	missense_variant	Exon 5 of 5	2		ENSP00000443410.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD3 exomes AF: 0.00000547 AC: 1 AN: 182877 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 67593

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000123

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 9.11e-7 AC: 1 AN: 1097764 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 363320

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: 0.00000119

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.088
BayesDel_addAF	Benign	-0.47	T
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.17
DEOGEN2	Benign	0.0059	T;T
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.76	T;.
M_CAP	Benign	0.0019	T
MetaRNN	Benign	0.064	T;T
MetaSVM	Benign	-0.96	T
PrimateAI	Benign	0.42	T
PROVEAN	Benign	0.61	N;N
REVEL	Benign	0.085
Sift	Benign	1.0	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.022	B;B
Vest4		0.040
MutPred		0.29		Loss of catalytic residue at T153 (P = 0.0306);Loss of catalytic residue at T153 (P = 0.0306);
MVP		0.15
MPC		0.32
ClinPred		0.029	T
GERP RS		2.2
Varity_R		0.054
gMVP		0.049

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

LitVar

Other links and lift over

dbSNP: rs1008391005; hg19: chrX-79698495;