chr5-6728882-A-G

Position:

• chr5-6728882-A-G

Variant summary

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

The NM_006999.6(TENT4A):​c.717-8628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,308 control chromosomes in the GnomAD database, including 1,534 homozygotes. 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 (1534 hom., cov: 33)
• Consequence: TENT4A NM_006999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

Genes affected

TENT4A (HGNC:16705): (terminal nucleotidyltransferase 4A) The protein encoded by this gene is a DNA polymerase that is likely involved in DNA repair. In addition, the encoded protein may be required for sister chromatid adhesion. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENT4A	NM_006999.6	c.717-8628A>G		intron_variant		ENST00000230859.8	NP_008930.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENT4A	ENST00000230859.8	c.717-8628A>G		intron_variant		1	NM_006999.6	ENSP00000230859.7
TENT4A	ENST00000631941.2	c.-34-8628A>G		intron_variant		5		ENSP00000488642.1
TENT4A	ENST00000515721.1	c.-34-8628A>G		intron_variant		3		ENSP00000427232.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18758 AN: 152190 Hom.: 1530 Cov.: 33

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.123 AC: 18764 AN: 152308 Hom.: 1534 Cov.: 33 AF XY: 0.129 AC XY: 9632 AN XY: 74464

Gnomad4 AFR AF: 0.0276

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.110

Alfa AF: 0.146 Hom.: 776

Bravo AF: 0.115

Asia WGS AF: 0.272 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.062
DANN	Benign	0.75

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: rs274700; hg19: chr5-6728995;