6-81622071-A-T

Variant names:

• chr6-81622071-A-T
• rs719144
• ENST00000412306.1:c.223-126958T>A

Variant summary

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

The ENST00000412306.1(TENT5A):​c.223-126958T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,072 control chromosomes in the GnomAD database, including 4,064 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 0.23 (4064 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 1 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]

RNA5SP210 (HGNC:43110): (RNA, 5S ribosomal pseudogene 210)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412306.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT5A	ENST00000412306.1	TSL:3	c.223-126958T>A		intron	N/A	ENSP00000401884.1	H0Y5Y3
	RNA5SP210	ENST00000391034.1	TSL:6	n.-129A>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34606 AN: 151950 Hom.: 4062 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.228 AC: 34638 AN: 152068 Hom.: 4064 Cov.: 31 AF XY: 0.230 AC XY: 17057 AN XY: 74308

African (AFR) AF: 0.226 AC: 9365 AN: 41476

American (AMR) AF: 0.253 AC: 3866 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5160

South Asian (SAS) AF: 0.182 AC: 880 AN: 4824

European-Finnish (FIN) AF: 0.292 AC: 3088 AN: 10572

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14725 AN: 67980

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.131 Hom.: 221

Bravo AF: 0.227

Asia WGS AF: 0.196 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.51
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs719144; hg19: chr6-82331788;