rs12138950

Variant names:

• chr1-19512621-A-C
• rs12138950
• ENST00000648702.1:c.-54+27966A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000648702.1(MICOS10):​c.-54+27966A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 146,418 control chromosomes in the GnomAD database, including 3 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 0.0052 (3 hom., cov: 31)
• Consequence: MICOS10 ENST00000648702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 21 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=-0.85).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00524 (767/146418) while in subpopulation AFR AF = 0.0161 (630/39178). AF 95% confidence interval is 0.015. There are 3 homozygotes in GnomAd4. There are 378 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

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+27966A>C		intron	N/A	ENSP00000497006.1	A0A3B3IRY5
	ENSG00000306287	ENST00000816783.1		n.523+10561T>G		intron	N/A
	ENSG00000306287	ENST00000816788.1		n.242-15283T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00521 AC: 763 AN: 146322 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.00680

Gnomad AMR AF: 0.00269

Gnomad ASJ AF: 0.000583

Gnomad EAS AF: 0.00653

Gnomad SAS AF: 0.00180

Gnomad FIN AF: 0.000196

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000556

Gnomad OTH AF: 0.00553

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

GnomAD4 genome AF: 0.00524 AC: 767 AN: 146418 Hom.: 3 Cov.: 31 AF XY: 0.00529 AC XY: 378 AN XY: 71398

African (AFR) AF: 0.0161 AC: 630 AN: 39178

American (AMR) AF: 0.00268 AC: 39 AN: 14532

Ashkenazi Jewish (ASJ) AF: 0.000583 AC: 2 AN: 3432

East Asian (EAS) AF: 0.00654 AC: 32 AN: 4890

South Asian (SAS) AF: 0.00181 AC: 8 AN: 4432

European-Finnish (FIN) AF: 0.000196 AC: 2 AN: 10228

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 284

European-Non Finnish (NFE) AF: 0.000556 AC: 37 AN: 66558

Other (OTH) AF: 0.00549 AC: 11 AN: 2002

Alfa AF: 0.159 Hom.: 7054

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.67
PhyloP100		0.17

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: rs12138950;

hg19: chr1-19839115;