rs7879396

Variant names:

• chrX-80370873-G-A
• rs7879396
• NM_001170574.2:c.-142+28309G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
TENT5D	NM_001170574.2	c.-142+28309G>A		intron_variant	Intron 3 of 4		NP_001164045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5D	ENST00000538312.5	c.-142+28309G>A		intron_variant	Intron 3 of 4	2		ENSP00000443410.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 13344 AN: 111051 Hom.: 901 Cov.: 23

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

African (AFR) AF: 0.105 AC: 3214 AN: 30657

American (AMR) AF: 0.245 AC: 2545 AN: 10405

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 264 AN: 2645

East Asian (EAS) AF: 0.480 AC: 1681 AN: 3499

South Asian (SAS) AF: 0.291 AC: 775 AN: 2667

European-Finnish (FIN) AF: 0.0961 AC: 567 AN: 5903

Middle Eastern (MID) AF: 0.107 AC: 22 AN: 206

European-Non Finnish (NFE) AF: 0.0759 AC: 4016 AN: 52927

Other (OTH) AF: 0.161 AC: 243 AN: 1509

Alfa AF: 0.109 Hom.: 2041

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
PhyloP100		-0.19
Mutation Taster		=100/0	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: rs7879396; hg19: chrX-79626372;