rs1509828

chr2-199984632-G-A

Variant summary

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

The XR_007088012.1(LOC124906112):n.435-12588C>T 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 0.138 in 152,078 control chromosomes in the GnomAD database, including 1,741 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 (1741 hom., cov: 32)
• Consequence: LOC124906112 XR_007088012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

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=-0.81).
• 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/exons	MANE	UniProt
LOC124906112	XR_007088012.1	n.435-12588C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAIP1	ENST00000435773.2	c.628-21111G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20951 AN: 151960 Hom.: 1743 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0760

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: 20947 AN: 152078 Hom.: 1741 Cov.: 32 AF XY: 0.132 AC XY: 9823 AN XY: 74324

Gnomad4 AFR AF: 0.0959

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0760

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.176

Alfa AF: 0.145 Hom.: 220

Bravo AF: 0.142

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1509828; hg19: chr2-200849355;