rs10799824

Variant names:

• chr1-19514680-G-A
• rs10799824
• ENST00000648702.1:c.-54+30025G>A

Variant summary

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

The ENST00000648702.1(MICOS10):​c.-54+30025G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,126 control chromosomes in the GnomAD database, including 2,585 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 0.18 (2585 hom., cov: 32)
• Consequence: MICOS10 ENST00000648702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 29 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=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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+30025G>A		intron	N/A	ENSP00000497006.1	A0A3B3IRY5
	ENSG00000306287	ENST00000816783.1		n.523+8502C>T		intron	N/A
	ENSG00000306287	ENST00000816788.1		n.242-17342C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26774 AN: 152008 Hom.: 2582 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.176 AC: 26801 AN: 152126 Hom.: 2585 Cov.: 32 AF XY: 0.172 AC XY: 12774 AN XY: 74366

African (AFR) AF: 0.242 AC: 10052 AN: 41472

American (AMR) AF: 0.180 AC: 2754 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3470

East Asian (EAS) AF: 0.131 AC: 678 AN: 5172

South Asian (SAS) AF: 0.115 AC: 554 AN: 4822

European-Finnish (FIN) AF: 0.100 AC: 1062 AN: 10600

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10518 AN: 68004

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.161 Hom.: 8316

Bravo AF: 0.182

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	19
DANN	Benign	0.71
PhyloP100		1.5

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: rs10799824;

hg19: chr1-19841174;