Genetic Variant MTPAP:n.970A>C (chr10-30367853-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000488290.5(MTPAP):n.970A>C 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 0.0799 in 1,378,300 control chromosomes in the GnomAD database, including 5,410 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 0.070 ( 525 hom., cov: 32)

Exomes 𝑓: 0.081 ( 4885 hom. )

Consequence

MTPAP
ENST00000488290.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.41

Variant links:

Genes affected

MTPAP (HGNC:25532): (mitochondrial poly(A) polymerase) The protein encoded by this gene is a member of the DNA polymerase type-B-like family. This enzyme synthesizes the 3' poly(A) tail of mitochondrial transcripts and plays a role in replication-dependent histone mRNA degradation.[provided by RefSeq, Jan 2011]

MTPAP links:

GOLGA2P6 (HGNC:44948): (GOLGA2 pseudogene 6)

GOLGA2P6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA2P6	NR_120609.1 link	n.1648A>C		non_coding_transcript_exon_variant	Exon 6 of 12

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MTPAP	ENST00000488290.5 link	n.970A>C	non_coding_transcript_exon_variant	Exon 6 of 17	2
GOLGA2P6	ENST00000340929.4 link	n.914+293A>C	intron_variant	Intron 7 of 13	6
MTPAP	ENST00000471055.1 link	n.1092+293A>C	intron_variant	Intron 6 of 9	5

Frequencies

GnomAD3 genomes

AF:

0.0704

AC:

10707

AN:

152104

Hom.:

525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0172

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0507

Gnomad ASJ

AF:

0.0683

Gnomad EAS

AF:

0.00618

Gnomad SAS

AF:

0.0817

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0994

Gnomad OTH

AF:

0.0554

GnomAD4 exome

AF:

0.0811

AC:

99486

AN:

1226078

Hom.:

4885

Cov.:

AF XY:

0.0825

AC XY:

51007

AN XY:

618592

show subpopulations

Gnomad4 AFR exome

AF:

0.0118

Gnomad4 AMR exome

AF:

0.0430

Gnomad4 ASJ exome

AF:

0.0627

Gnomad4 EAS exome

AF:

0.00292

Gnomad4 SAS exome

AF:

0.0864

Gnomad4 FIN exome

AF:

0.142

Gnomad4 NFE exome

AF:

0.0863

Gnomad4 OTH exome

AF:

0.0763

GnomAD4 genome

AF:

0.0703

AC:

10708

AN:

152222

Hom.:

525

Cov.:

AF XY:

0.0719

AC XY:

5352

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0171

Gnomad4 AMR

AF:

0.0507

Gnomad4 ASJ

AF:

0.0683

Gnomad4 EAS

AF:

0.00619

Gnomad4 SAS

AF:

0.0824

Gnomad4 FIN

AF:

0.152

Gnomad4 NFE

AF:

0.0994

Gnomad4 OTH

AF:

0.0553

Alfa

AF:

0.0761

Hom.:

135

Bravo

AF:

0.0584

Asia WGS

AF:

0.0430

AC:

151

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

9.6

DANN

Benign

0.81

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over