10-23255343-T-C

Position:

• chr10-23255343-T-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.1201-4652A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,194 control chromosomes in the GnomAD database, including 28,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.60 (28036 hom., cov: 34)
• Consequence: C10orf67 NM_001371909.1 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -1.16

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 10-23255343-T-C is Benign according to our data. Variant chr10-23255343-T-C is described in ClinVar as [Benign]. Clinvar id is 444145.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf67	NM_001371909.1	c.1201-4652A>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.1201-4652A>G		intron_variant		5	NM_001371909.1	ENSP00000490528.2
C10orf67	ENST00000376501.7	n.1120-4652A>G		intron_variant		5		ENSP00000490237.1

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90591 AN: 152076 Hom.: 27989 Cov.: 34

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.596 AC: 90693 AN: 152194 Hom.: 28036 Cov.: 34 AF XY: 0.598 AC XY: 44473 AN XY: 74408

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.601

Alfa AF: 0.546 Hom.: 2923

Bravo AF: 0.620

Asia WGS AF: 0.717 AC: 2492 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	-0.77
CADD	Benign	0.12
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7904665; hg19: chr10-23544272;