chrX-80443094-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -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. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. 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 NM_152630.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 25 publications found

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

Our verdict: Likely_benign. The variant received -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

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

GnomAD2 exomes AF: 0.559 AC: 101844 AN: 182198 AF XY: 0.551

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 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

African (AFR) AF: 0.375 AC: 9900 AN: 26379

American (AMR) AF: 0.532 AC: 18665 AN: 35086

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 12604 AN: 19348

East Asian (EAS) AF: 0.0646 AC: 1950 AN: 30197

South Asian (SAS) AF: 0.286 AC: 15475 AN: 54125

European-Finnish (FIN) AF: 0.665 AC: 26914 AN: 40497

Middle Eastern (MID) AF: 0.545 AC: 2252 AN: 4134

European-Non Finnish (NFE) AF: 0.716 AC: 602594 AN: 841728

Other (OTH) AF: 0.604 AC: 27794 AN: 46054

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

African (AFR) AF: 0.380 AC: 11516 AN: 30334

American (AMR) AF: 0.561 AC: 5752 AN: 10247

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 1724 AN: 2632

East Asian (EAS) AF: 0.0899 AC: 313 AN: 3483

South Asian (SAS) AF: 0.252 AC: 662 AN: 2625

European-Finnish (FIN) AF: 0.645 AC: 3748 AN: 5815

Middle Eastern (MID) AF: 0.606 AC: 131 AN: 216

European-Non Finnish (NFE) AF: 0.713 AC: 37439 AN: 52527

Other (OTH) AF: 0.556 AC: 825 AN: 1484

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
PhyloP100		-0.67
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
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

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