rs10917468

chr1-19516860-T-C

Variant summary

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

The XR_947017.3(LOC105376817):n.293+1223A>G 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 0.311 in 152,058 control chromosomes in the GnomAD database, including 8,280 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 0.31 (8280 hom., cov: 32)
• Consequence: LOC105376817 XR_947017.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30

Genes affected

LOC105376817 (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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376817	XR_947017.3	n.293+1223A>G		intron_variant, non_coding_transcript_variant
LOC105376819	XR_001737920.2	n.144-1261T>C		intron_variant, non_coding_transcript_variant
LOC105376819	XR_947019.1	n.189-1261T>C		intron_variant, non_coding_transcript_variant
LOC105376819	XR_947020.3	n.144-1261T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICOS10	ENST00000648702.1	c.-54+32205T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47148 AN: 151940 Hom.: 8261 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.311 AC: 47221 AN: 152058 Hom.: 8280 Cov.: 32 AF XY: 0.310 AC XY: 23036 AN XY: 74340

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.307

Alfa AF: 0.240 Hom.: 5460

Bravo AF: 0.324

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.30
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10917468; hg19: chr1-19843354;