rs12410532

Variant names:

• chr1-19518785-C-T
• rs12410532
• ENST00000648702.1:c.-54+34130C>T

Variant summary

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

The ENST00000648702.1(MICOS10):​c.-54+34130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,962 control chromosomes in the GnomAD database, including 2,368 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 0.17 (2368 hom., cov: 30)
• Consequence: MICOS10 ENST00000648702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 5 publications found

Genes affected

MICOS10 (HGNC:32068): (mitochondrial contact site and cristae organizing system subunit 10) Predicted to be involved in inner mitochondrial membrane organization. Located in mitochondrion. Part of MIB complex; MICOS complex; and SAM complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000306287 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376819	XR_001737920.2	n.247+561C>T		intron_variant	Intron 2 of 2
LOC105376817	XR_947017.3	n.232-641G>A		intron_variant	Intron 2 of 3
LOC105376819	XR_947019.1	n.292+561C>T		intron_variant	Intron 3 of 3
LOC105376819	XR_947020.3	n.247+561C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICOS10	ENST00000648702.1	c.-54+34130C>T		intron_variant	Intron 1 of 3			ENSP00000497006.1
ENSG00000306287	ENST00000816783.1	n.523+4397G>A		intron_variant	Intron 2 of 2
ENSG00000306287	ENST00000816788.1	n.242-21447G>A		intron_variant	Intron 1 of 1
ENSG00000306287	ENST00000816790.1	n.358-21447G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25877 AN: 151844 Hom.: 2367 Cov.: 30

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.170 AC: 25901 AN: 151962 Hom.: 2368 Cov.: 30 AF XY: 0.166 AC XY: 12329 AN XY: 74294

African (AFR) AF: 0.222 AC: 9184 AN: 41428

American (AMR) AF: 0.179 AC: 2729 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3464

East Asian (EAS) AF: 0.134 AC: 693 AN: 5160

South Asian (SAS) AF: 0.117 AC: 561 AN: 4808

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10576

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10493 AN: 67952

Other (OTH) AF: 0.169 AC: 358 AN: 2114

Alfa AF: 0.168 Hom.: 292

Bravo AF: 0.176

Asia WGS AF: 0.157 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.75
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12410532; hg19: chr1-19845279;