rs4448140

Variant names:

• chr6-81559036-A-C
• rs4448140
• ENST00000412306.1:c.223-63923T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-81559036-A-C
• chr6-81559036-A-G
• chr6-81559036-A-T

Variant summary

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

The ENST00000412306.1(TENT5A):​c.223-63923T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,796 control chromosomes in the GnomAD database, including 9,076 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 0.34 (9076 hom., cov: 32)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 3 publications found

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]

TENT5A Gene-Disease associations (from GenCC):

• osteogenesis imperfecta, type 18

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• osteogenesis imperfecta

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000303042 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5A	ENST00000412306.1	c.223-63923T>G		intron_variant	Intron 1 of 2	3		ENSP00000401884.1
ENSG00000303042	ENST00000791451.1	n.41+941A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50852 AN: 151678 Hom.: 9065 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.335 AC: 50895 AN: 151796 Hom.: 9076 Cov.: 32 AF XY: 0.337 AC XY: 24970 AN XY: 74176

African (AFR) AF: 0.226 AC: 9344 AN: 41418

American (AMR) AF: 0.445 AC: 6762 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1688 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2220 AN: 5164

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4165 AN: 10512

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23883 AN: 67918

Other (OTH) AF: 0.390 AC: 819 AN: 2102

Alfa AF: 0.360 Hom.: 15073

Bravo AF: 0.337

Asia WGS AF: 0.396 AC: 1368 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs4448140; hg19: chr6-82268753;