2-200004203-A-G

Position:

• chr2-200004203-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007088012.1(LOC124906112):​n.434+6488T>C 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 0.732 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: LOC124906112 XR_007088012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

Genes affected

LOC124906112 (HGNC:):

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906112	XR_007088012.1	n.434+6488T>C		intron_variant, non_coding_transcript_variant
LOC124906112	XR_007088015.1	n.435-4289T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAIP1	ENST00000435773.2	c.628-1540A>G		intron_variant		3		ENSP00000396846

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

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.703

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7565480; hg19: chr2-200868926;