1-19517082-A-G

Variant names:

• chr1-19517082-A-G
• rs10917469
• ENST00000648702.1:c.-54+32427A>G

Variant summary

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

The ENST00000648702.1(MICOS10):​c.-54+32427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,126 control chromosomes in the GnomAD database, including 2,610 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 (2610 hom., cov: 32)
• Consequence: MICOS10 ENST00000648702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694
• Publications: 19 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICOS10	ENST00000648702.1		c.-54+32427A>G		intron	N/A	ENSP00000497006.1
	ENSG00000306287	ENST00000816783.1		n.523+6100T>C		intron	N/A
	ENSG00000306287	ENST00000816788.1		n.242-19744T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26847 AN: 152008 Hom.: 2607 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.177 AC: 26875 AN: 152126 Hom.: 2610 Cov.: 32 AF XY: 0.172 AC XY: 12824 AN XY: 74394

African (AFR) AF: 0.243 AC: 10105 AN: 41506

American (AMR) AF: 0.181 AC: 2766 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3470

East Asian (EAS) AF: 0.134 AC: 693 AN: 5174

South Asian (SAS) AF: 0.117 AC: 564 AN: 4826

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10598

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

European-Non Finnish (NFE) AF: 0.154 AC: 10497 AN: 67970

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.0993 Hom.: 172

Bravo AF: 0.183

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.7
DANN	Benign	0.87
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs10917469; hg19: chr1-19843576;