rs554643599

Variant names:

• chr2-199961847-CT-C
• NM_001394955.1:c.719delT

Your query was ambiguous. Multiple possible variants found:

• chr2-199961847-CT-C
• chr2-199961847-CT-CTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001394955.1(MAIP1):​c.719delT​(p.Leu240fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,674 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: MAIP1 NM_001394955.1 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAIP1	NM_001394955.1	c.719delT	p.Leu240fs	frameshift_variant	Exon 4 of 5	ENST00000392290.6	NP_001381884.1
MAIP1	NM_024520.3	c.719delT	p.Leu240fs	frameshift_variant	Exon 5 of 6		NP_078796.2
MAIP1	NM_001369399.1	c.650-1883delT		intron_variant	Intron 4 of 4		NP_001356328.1
MAIP1	NR_161377.1	n.972-116delT		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAIP1	ENST00000392290.6	c.719delT	p.Leu240fs	frameshift_variant	Exon 4 of 5	1	NM_001394955.1	ENSP00000376111.1
MAIP1	ENST00000295079.6	c.719delT	p.Leu240fs	frameshift_variant	Exon 5 of 6	2		ENSP00000295079.2
MAIP1	ENST00000435773.2	c.625+1970delT		intron_variant	Intron 3 of 4	3		ENSP00000396846.2
MAIP1	ENST00000469156.1	n.202-1883delT		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461674 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 727140

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: chr2-200826570;