NM_001394955.1:c.451-929T>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001394955.1(MAIP1):​c.451-929T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

MAIP1
NM_001394955.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.462
Variant links:
Genes affected
MAIP1 (HGNC:26198): (matrix AAA peptidase interacting protein 1) Predicted to enable ribosome binding activity. Involved in calcium import into the mitochondrion; mitochondrial calcium ion homeostasis; and protein insertion into mitochondrial membrane. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAIP1NM_001394955.1 linkc.451-929T>G intron_variant Intron 1 of 4 ENST00000392290.6 NP_001381884.1
MAIP1NM_024520.3 linkc.451-929T>G intron_variant Intron 2 of 5 NP_078796.2 Q8WWC4A0A024R3U8
MAIP1NM_001369399.1 linkc.451-929T>G intron_variant Intron 2 of 4 NP_001356328.1
MAIP1NR_161377.1 linkn.773-929T>G intron_variant Intron 2 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAIP1ENST00000392290.6 linkc.451-929T>G intron_variant Intron 1 of 4 1 NM_001394955.1 ENSP00000376111.1 Q8WWC4
MAIP1ENST00000295079.6 linkc.451-929T>G intron_variant Intron 2 of 5 2 ENSP00000295079.2 Q8WWC4
MAIP1ENST00000435773.2 linkc.427-929T>G intron_variant Intron 1 of 4 3 ENSP00000396846.2 H7C0V0

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.0
DANN
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-200823062; API