rs1113265

Variant names:

• chrX-80443094-C-G
• rs1113265
• NM_152630.5:c.555C>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_152630.5(TENT5D):​c.555C>G​(p.Asp185Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/18 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

• Frequency:
  • Genomes: 𝑓 0.57 (13984 hom., 17919 hem., cov: 23)
  • Exomes 𝑓: 0.65 (168092 hom. 232773 hem.)
  • Failed GnomAD Quality Control
• Consequence: TENT5D NM_152630.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=3.311974E-5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT5D	NM_152630.5	c.555C>G	p.Asp185Glu	missense_variant	Exon 3 of 3	ENST00000308293.6	NP_689843.1
TENT5D	NM_001170574.2	c.555C>G	p.Asp185Glu	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.555C>G	p.Asp185Glu	missense_variant	Exon 3 of 3	1	NM_152630.5	ENSP00000308575.5
TENT5D	ENST00000538312.5	c.555C>G	p.Asp185Glu	missense_variant	Exon 5 of 5	2		ENSP00000443410.1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 62616 AN: 109986 Hom.: 13994 Cov.: 23 AF XY: 0.553 AC XY: 17896 AN XY: 32376

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.629

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.559

GnomAD3 exomes AF: 0.559 AC: 101844 AN: 182198 Hom.: 20579 AF XY: 0.551 AC XY: 36904 AN XY: 66980

Gnomad AFR exome AF: 0.378

Gnomad AMR exome AF: 0.528

Gnomad ASJ exome AF: 0.657

Gnomad EAS exome AF: 0.0916

Gnomad SAS exome AF: 0.282

Gnomad FIN exome AF: 0.662

Gnomad NFE exome AF: 0.711

Gnomad OTH exome AF: 0.611

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.654 AC: 718148 AN: 1097548 Hom.: 168092 Cov.: 46 AF XY: 0.641 AC XY: 232773 AN XY: 363178

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.532

Gnomad4 ASJ exome AF: 0.651

Gnomad4 EAS exome AF: 0.0646

Gnomad4 SAS exome AF: 0.286

Gnomad4 FIN exome AF: 0.665

Gnomad4 NFE exome AF: 0.716

Gnomad4 OTH exome AF: 0.604

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.569 AC: 62624 AN: 110041 Hom.: 13984 Cov.: 23 AF XY: 0.552 AC XY: 17919 AN XY: 32441

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.0899

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.556

Alfa AF: 0.660 Hom.: 25531

Bravo AF: 0.558

TwinsUK AF: 0.718 AC: 2662

ALSPAC AF: 0.734 AC: 2120

ESP6500AA AF: 0.391 AC: 1500

ESP6500EA AF: 0.710 AC: 4774

ExAC AF: 0.554 AC: 67287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-1.0	T
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.50
DEOGEN2	Benign	0.013	T;T
FATHMM_MKL	Benign	0.11	N
LIST_S2	Benign	0.13	T;.
MetaRNN	Benign	0.000033	T;T
MetaSVM	Benign	-0.93	T
PrimateAI	Benign	0.31	T
PROVEAN	Benign	0.57	N;N
REVEL	Benign	0.074
Sift	Benign	1.0	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0010	B;B
Vest4		0.017
MutPred		0.097		Gain of methylation at K190 (P = 0.1679);Gain of methylation at K190 (P = 0.1679);
MPC		0.33
ClinPred		0.012	T
GERP RS		-8.8
Varity_R		0.052
gMVP		0.078

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: rs1113265; hg19: chrX-79698593; COSMIC: COSV57635595;