rs11818836

Variant summary

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

The ENST00000488290.5(MTPAP):​n.1913-10565A>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 0.406 in 152,110 control chromosomes in the GnomAD database, including 15,458 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 0.41 ( 15458 hom., cov: 32)

Consequence

MTPAP
ENST00000488290.5 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.401
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]

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=-0.71).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTPAPENST00000488290.5 linkuse as main transcriptn.1913-10565A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.406
AC:
61687
AN:
151990
Hom.:
15455
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.449
Gnomad AMR
AF:
0.526
Gnomad ASJ
AF:
0.550
Gnomad EAS
AF:
0.174
Gnomad SAS
AF:
0.420
Gnomad FIN
AF:
0.488
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.552
Gnomad OTH
AF:
0.450
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.406
AC:
61688
AN:
152110
Hom.:
15458
Cov.:
32
AF XY:
0.405
AC XY:
30098
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.526
Gnomad4 ASJ
AF:
0.550
Gnomad4 EAS
AF:
0.174
Gnomad4 SAS
AF:
0.421
Gnomad4 FIN
AF:
0.488
Gnomad4 NFE
AF:
0.552
Gnomad4 OTH
AF:
0.445
Alfa
AF:
0.512
Hom.:
9553
Bravo
AF:
0.397
Asia WGS
AF:
0.287
AC:
1001
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
6.0
DANN
Benign
0.94

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.

Other links and lift over

dbSNP: rs11818836; hg19: chr10-30641134; API