rs10917469

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-19517082-A-G
• chr1-19517082-A-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+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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376819	XR_001737920.2	n.144-1039A>G		intron_variant	Intron 1 of 2
LOC105376817	XR_947017.3	n.293+1001T>C		intron_variant	Intron 3 of 3
LOC105376819	XR_947019.1	n.189-1039A>G		intron_variant	Intron 2 of 3
LOC105376819	XR_947020.3	n.144-1039A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICOS10	ENST00000648702.1	c.-54+32427A>G		intron_variant	Intron 1 of 3			ENSP00000497006.1
ENSG00000306287	ENST00000816783.1	n.523+6100T>C		intron_variant	Intron 2 of 2
ENSG00000306287	ENST00000816788.1	n.242-19744T>C		intron_variant	Intron 1 of 1
ENSG00000306287	ENST00000816790.1	n.358-19744T>C		intron_variant	Intron 2 of 2

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 v4.3

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;