ENST00000648702.1:c.-54+16631G>A

Variant names:

• chr1-19501286-G-A
• rs6683419
• ENST00000648702.1:c.-54+16631G>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+16631G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,834 control chromosomes in the GnomAD database, including 21,096 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 0.53 (21096 hom., cov: 30)
• Consequence: MICOS10 ENST00000648702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.705 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICOS10	ENST00000648702.1		c.-54+16631G>A		intron	N/A	ENSP00000497006.1
	ENSG00000306287	ENST00000816783.1		n.524-3948C>T		intron	N/A
	ENSG00000306287	ENST00000816788.1		n.242-3948C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79679 AN: 151716 Hom.: 21087 Cov.: 30

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.525 AC: 79726 AN: 151834 Hom.: 21096 Cov.: 30 AF XY: 0.526 AC XY: 39004 AN XY: 74216

African (AFR) AF: 0.515 AC: 21284 AN: 41348

American (AMR) AF: 0.541 AC: 8248 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1728 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3745 AN: 5168

South Asian (SAS) AF: 0.567 AC: 2732 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5189 AN: 10548

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34912 AN: 67938

Other (OTH) AF: 0.554 AC: 1166 AN: 2106

Alfa AF: 0.519 Hom.: 10447

Bravo AF: 0.527

Asia WGS AF: 0.633 AC: 2201 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	7.6
DANN	Benign	0.58
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6683419; hg19: chr1-19827780;