10-23283453-A-C

Position:

• chr10-23283453-A-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_001371909.1(C10orf67):​c.910-1375T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,162 control chromosomes in the GnomAD database, including 54,745 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.84 (54745 hom., cov: 32)
• Consequence: C10orf67 NM_001371909.1 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.0750

Genes affected

C10orf67 (HGNC:28716): (chromosome 10 open reading frame 67) Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

C10orf67 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 10-23283453-A-C is Benign according to our data. Variant chr10-23283453-A-C is described in ClinVar as [Benign]. Clinvar id is 444144.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf67	NM_001371909.1	c.910-1375T>G		intron_variant		ENST00000636213.3	NP_001358838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf67	ENST00000636213.3	c.910-1375T>G		intron_variant		5	NM_001371909.1	ENSP00000490528.2
C10orf67	ENST00000376500.5	c.763-1375T>G		intron_variant		5		ENSP00000365683.1
C10orf67	ENST00000376501.7	n.829-1375T>G		intron_variant		5		ENSP00000490237.1

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127580 AN: 152044 Hom.: 54704 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.839 AC: 127678 AN: 152162 Hom.: 54745 Cov.: 32 AF XY: 0.836 AC XY: 62179 AN XY: 74400

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.832

Alfa AF: 0.896 Hom.: 58739

Bravo AF: 0.823

Asia WGS AF: 0.640 AC: 2226 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Type 2 diabetes mellitus Benign:1

Benign, no assertion criteria provided

case-control

Diabetes Molecular Genetics Section, Phoenix Epidemiology and Clinical Research Branch, National Institutes of Health

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4454613; hg19: chr10-23572382;