12-98515429-C-T

Variant names:

• chr12-98515429-C-T
• rs117151045
• ENST00000548760.2:n.901G>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000548760.2(TMPO-AS1):​n.901G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 178,054 control chromosomes in the GnomAD database, including 643 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.070 (533 hom., cov: 33)
  • Exomes 𝑓: 0.072 (110 hom.)
• Consequence: TMPO-AS1 ENST00000548760.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.597

Genes affected

TMPO-AS1 (HGNC:44158): (TMPO antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 12-98515429-C-T is Benign according to our data. Variant chr12-98515429-C-T is described in ClinVar as [Benign]. Clinvar id is 684009.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMPO-AS1	NR_027157.1	n.705G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMPO-AS1	ENST00000548760.2	n.901G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
TMPO-AS1	ENST00000546421.2	n.642-39G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10712 AN: 152010 Hom.: 531 Cov.: 33

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00136

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.0702

GnomAD4 exome AF: 0.0719 AC: 1865 AN: 25928 Hom.: 110 Cov.: 0 AF XY: 0.0767 AC XY: 1057 AN XY: 13786

Gnomad4 AFR exome AF: 0.0123

Gnomad4 AMR exome AF: 0.0421

Gnomad4 ASJ exome AF: 0.0564

Gnomad4 EAS exome AF: 0.00100

Gnomad4 SAS exome AF: 0.131

Gnomad4 FIN exome AF: 0.0635

Gnomad4 NFE exome AF: 0.0658

Gnomad4 OTH exome AF: 0.0678

GnomAD4 genome AF: 0.0704 AC: 10704 AN: 152126 Hom.: 533 Cov.: 33 AF XY: 0.0713 AC XY: 5302 AN XY: 74360

Gnomad4 AFR AF: 0.0179

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0964

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0477 Hom.: 47

Bravo AF: 0.0628

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117151045; hg19: chr12-98909207;