rs12084204

Positions:

• chr1-19506073-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065522.1(LOC105376819):​n.310+5710C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,098 control chromosomes in the GnomAD database, including 7,308 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 0.30 (7308 hom., cov: 33)
• Consequence: LOC105376819 XR_007065522.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

LOC105376819 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376819	XR_007065522.1	n.310+5710C>T		intron_variant, non_coding_transcript_variant
LOC105376819	XR_001737920.2	n.143+5710C>T		intron_variant, non_coding_transcript_variant
LOC105376819	XR_947019.1	n.143+5710C>T		intron_variant, non_coding_transcript_variant
LOC105376819	XR_947020.3	n.143+5710C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICOS10	ENST00000648702.1	c.-54+21418C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45630 AN: 151980 Hom.: 7311 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.300 AC: 45645 AN: 152098 Hom.: 7308 Cov.: 33 AF XY: 0.306 AC XY: 22749 AN XY: 74352

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.321

Alfa AF: 0.321 Hom.: 9344

Bravo AF: 0.293

Asia WGS AF: 0.433 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12084204; hg19: chr1-19832567;