rs10497843

Variant names:

• chr2-199967140-C-G
• rs10497843
• ENST00000435773.2:c.625+7260C>G

Variant summary

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

The ENST00000435773.2(MAIP1):​c.625+7260C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,186 control chromosomes in the GnomAD database, including 1,749 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 0.14 (1749 hom., cov: 32)
• Consequence: MAIP1 ENST00000435773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887
• Publications: 0 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAIP1	ENST00000435773.2	c.625+7260C>G		intron_variant	Intron 3 of 4	3		ENSP00000396846.2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21046 AN: 152068 Hom.: 1751 Cov.: 32

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.138 AC: 21045 AN: 152186 Hom.: 1749 Cov.: 32 AF XY: 0.133 AC XY: 9871 AN XY: 74404

African (AFR) AF: 0.0981 AC: 4076 AN: 41550

American (AMR) AF: 0.144 AC: 2197 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3462

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0748 AC: 361 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1315 AN: 10594

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11644 AN: 67970

Other (OTH) AF: 0.177 AC: 372 AN: 2106

Alfa AF: 0.145 Hom.: 220

Bravo AF: 0.143

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.68
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs10497843; hg19: chr2-200831863;