rs11951576

Variant names:

• chr5-6731300-C-T
• rs11951576
• NM_006999.6:c.717-6210C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006999.6(TENT4A):​c.717-6210C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,036 control chromosomes in the GnomAD database, including 5,878 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 0.26 (5878 hom., cov: 33)
• Consequence: TENT4A NM_006999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT4A	NM_006999.6	c.717-6210C>T		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.717-6210C>T		intron_variant	Intron 1 of 12	1	NM_006999.6	ENSP00000230859.7
TENT4A	ENST00000631941.2	c.-34-6210C>T		intron_variant	Intron 1 of 12	5		ENSP00000488642.1
TENT4A	ENST00000515721.1	c.-34-6210C>T		intron_variant	Intron 1 of 1	3		ENSP00000427232.1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39785 AN: 151918 Hom.: 5871 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.262 AC: 39795 AN: 152036 Hom.: 5878 Cov.: 33 AF XY: 0.267 AC XY: 19856 AN XY: 74328

African (AFR) AF: 0.114 AC: 4708 AN: 41458

American (AMR) AF: 0.316 AC: 4827 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3460

East Asian (EAS) AF: 0.394 AC: 2034 AN: 5168

South Asian (SAS) AF: 0.347 AC: 1672 AN: 4820

European-Finnish (FIN) AF: 0.347 AC: 3655 AN: 10548

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21029 AN: 67984

Other (OTH) AF: 0.285 AC: 601 AN: 2112

Alfa AF: 0.282 Hom.: 1137

Bravo AF: 0.253

Asia WGS AF: 0.301 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.94
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: rs11951576; hg19: chr5-6731413;