rs7879396

chrX-80370873-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170574.2(TENT5D):c.-142+28309G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 111,100 control chromosomes in the GnomAD database, including 902 homozygotes. There are 4,094 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (902 hom., 4094 hem., cov: 23)
• Consequence: TENT5D NM_001170574.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENT5D	NM_001170574.2	c.-142+28309G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENT5D	ENST00000538312.5	c.-142+28309G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 13344 AN: 111051 Hom.: 901 Cov.: 23 AF XY: 0.123 AC XY: 4093 AN XY: 33319

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0367

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.156

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.120 AC: 13352 AN: 111100 Hom.: 902 Cov.: 23 AF XY: 0.123 AC XY: 4094 AN XY: 33378

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.0998

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.161

Alfa AF: 0.0942 Hom.: 844

Bravo AF: 0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.27
Dann	Benign	0.19

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: rs7879396; hg19: chrX-79626372;