rs140244380

Variant names:

• chrX-80442672-C-G
• rs140244380
• NM_152630.5:c.133C>G

Your query was ambiguous. Multiple possible variants found:

• chrX-80442672-C-G
• chrX-80442672-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152630.5(TENT5D):​c.133C>G​(p.His45Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,420 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. 13/20 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. H45Y) has been classified as Uncertain significance.

• 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: 1.75
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16518322).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT5D	NM_152630.5	c.133C>G	p.His45Asp	missense_variant	Exon 3 of 3	ENST00000308293.6	NP_689843.1
TENT5D	NM_001170574.2	c.133C>G	p.His45Asp	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.133C>G	p.His45Asp	missense_variant	Exon 3 of 3	1	NM_152630.5	ENSP00000308575.5
TENT5D	ENST00000538312.5	c.133C>G	p.His45Asp	missense_variant	Exon 5 of 5	2		ENSP00000443410.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 9.11e-7 AC: 1 AN: 1097420 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 363090

African (AFR) AF: 0.00 AC: 0 AN: 26373

American (AMR) AF: 0.00 AC: 0 AN: 35150

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19347

East Asian (EAS) AF: 0.00 AC: 0 AN: 30187

South Asian (SAS) AF: 0.00 AC: 0 AN: 54114

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40502

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4133

European-Non Finnish (NFE) AF: 0.00000119 AC: 1 AN: 841560

Other (OTH) AF: 0.00 AC: 0 AN: 46054

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Uncertain	0.98
DEOGEN2	Benign	0.028	T;T
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.77	T;.
M_CAP	Benign	0.0061	T
MetaRNN	Benign	0.17	T;T
MetaSVM	Benign	-1.1	T
PhyloP100		1.7
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-0.40	N;N
REVEL	Benign	0.069
Sift	Benign	0.11	T;T
Sift4G	Benign	0.30	T;T
Polyphen		0.17	B;B
Vest4		0.43
MutPred		0.35		Loss of methylation at K48 (P = 0.1033);Loss of methylation at K48 (P = 0.1033);
MVP		0.55
MPC		0.70
ClinPred		0.10	T
GERP RS		3.5
Varity_R		0.16
gMVP		0.71
Mutation Taster		=92/8	polymorphism

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: rs140244380; hg19: chrX-79698171;