chr6-81515245-A-G

Position:

• chr6-81515245-A-G

Variant summary

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

The ENST00000412306.1(TENT5A):​c.223-20132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 150,846 control chromosomes in the GnomAD database, including 3,874 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 0.21 (3874 hom., cov: 30)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

TENT5A (HGNC:18345): (terminal nucleotidyltransferase 5A) Enables RNA binding activity. Predicted to be involved in mRNA stabilization. Predicted to act upstream of or within response to bacterium. Implicated in lung non-small cell carcinoma; osteoarthritis; and osteogenesis imperfecta type 18. [provided by Alliance of Genome Resources, Apr 2022]

LOC105377871 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377871	XR_001744222.2	n.22394T>C		non_coding_transcript_exon_variant	1/4
LOC105377871	XR_007059657.1	n.15366T>C		non_coding_transcript_exon_variant	2/5
LOC105377871	XR_007059658.1	n.22394T>C		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENT5A	ENST00000412306.1	c.223-20132T>C		intron_variant		3		ENSP00000401884.1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32137 AN: 150730 Hom.: 3874 Cov.: 30

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.213 AC: 32143 AN: 150846 Hom.: 3874 Cov.: 30 AF XY: 0.215 AC XY: 15792 AN XY: 73586

Gnomad4 AFR AF: 0.0989

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.243

Alfa AF: 0.242 Hom.: 2540

Bravo AF: 0.206

Asia WGS AF: 0.234 AC: 811 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.081
DANN	Benign	0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9449341; hg19: chr6-82224962;