rs1113265

Positions:

• chrX-80443094-C-G

Variant summary

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

The ENST00000308293.6(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 same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D185V) has been classified as Uncertain significance.

• 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 ENST00000308293.6 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/exons	MANE	Protein	UniProt
TENT5D	NM_152630.5	c.555C>G	p.Asp185Glu	missense_variant	3/3	ENST00000308293.6	NP_689843.1
TENT5D	NM_001170574.2	c.555C>G	p.Asp185Glu	missense_variant	5/5		NP_001164045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENT5D	ENST00000308293.6	c.555C>G	p.Asp185Glu	missense_variant	3/3	1	NM_152630.5	ENSP00000308575	P1
TENT5D	ENST00000538312.5	c.555C>G	p.Asp185Glu	missense_variant	5/5	2		ENSP00000443410	P1

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
MutationTaster	Benign	1.0	P;P
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;