rs10485393

chr6-81494795-G-C

Variant summary

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

The XR_007059658.1(LOC105377871):n.23042+239C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 152,088 control chromosomes in the GnomAD database, including 128 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 0.041 (128 hom., cov: 31)
• Consequence: LOC105377871 XR_007059658.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

Genes affected

LOC105377871 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377871	XR_007059658.1	n.23042+239C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENT5A	ENST00000412306.1	c.*38+239C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6287 AN: 151970 Hom.: 127 Cov.: 31

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0414 AC: 6298 AN: 152088 Hom.: 128 Cov.: 31 AF XY: 0.0401 AC XY: 2984 AN XY: 74362

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.00836

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.0463 Hom.: 25

Bravo AF: 0.0405

Asia WGS AF: 0.0420 AC: 146 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.31
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485393; hg19: chr6-82204512;