2-200004203-A-G

Variant names:

• chr2-200004203-A-G
• rs7565480
• ENST00000435773.2:c.626-1540A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435773.2(MAIP1):​c.626-1540A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,052 control chromosomes in the GnomAD database, including 41,267 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 0.73 (41267 hom., cov: 31)
• Consequence: MAIP1 ENST00000435773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 5 publications found

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]

LOC124906112 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435773.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAIP1	ENST00000435773.2	TSL:3	c.626-1540A>G		intron	N/A	ENSP00000396846.2

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111114 AN: 151934 Hom.: 41206 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.700

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.732 AC: 111236 AN: 152052 Hom.: 41267 Cov.: 31 AF XY: 0.736 AC XY: 54685 AN XY: 74296

African (AFR) AF: 0.832 AC: 34535 AN: 41488

American (AMR) AF: 0.769 AC: 11737 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2373 AN: 3464

East Asian (EAS) AF: 0.782 AC: 4037 AN: 5164

South Asian (SAS) AF: 0.839 AC: 4047 AN: 4826

European-Finnish (FIN) AF: 0.662 AC: 6996 AN: 10564

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45364 AN: 67970

Other (OTH) AF: 0.703 AC: 1480 AN: 2104

Alfa AF: 0.705 Hom.: 5753

Bravo AF: 0.738

Asia WGS AF: 0.821 AC: 2852 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.47
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7565480; hg19: chr2-200868926;