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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648702.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICOS10	ENST00000648702.1		c.-54+34130C>T		intron	N/A	ENSP00000497006.1	A0A3B3IRY5
	ENSG00000306287	ENST00000816783.1		n.523+4397G>A		intron	N/A
	ENSG00000306287	ENST00000816788.1		n.242-21447G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12410532;

hg19: chr1-19845279;