chr5-6728882-A-G

Variant names:

• chr5-6728882-A-G
• rs274700
• NM_006999.6:c.717-8628A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TENT4A	NM_006999.6	c.717-8628A>G		intron_variant	Intron 1 of 12	ENST00000230859.8	NP_008930.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT4A	ENST00000230859.8	c.717-8628A>G		intron_variant	Intron 1 of 12	1	NM_006999.6	ENSP00000230859.7
TENT4A	ENST00000631941.2	c.-34-8628A>G		intron_variant	Intron 1 of 12	5		ENSP00000488642.1
TENT4A	ENST00000515721.1	c.-34-8628A>G		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.0276 AC: 1146 AN: 41584

American (AMR) AF: 0.169 AC: 2594 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1482 AN: 5184

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4824

European-Finnish (FIN) AF: 0.188 AC: 1991 AN: 10598

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9837 AN: 68018

Other (OTH) AF: 0.110 AC: 232 AN: 2116

Alfa AF: 0.147 Hom.: 1079

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
PhyloP100		-0.80
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: rs274700; hg19: chr5-6728995;