chr10-23310629-C-A

Position:

• chr10-23310629-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001371909.1(C10orf67):​c.547-7170G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: C10orf67 NM_001371909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf67	NM_001371909.1	c.547-7170G>T		intron_variant		ENST00000636213.3	NP_001358838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf67	ENST00000636213.3	c.547-7170G>T		intron_variant		5	NM_001371909.1	ENSP00000490528.2
C10orf67	ENST00000376500.5	c.400-7170G>T		intron_variant		5		ENSP00000365683.1
C10orf67	ENST00000649478.1	c.451-7170G>T		intron_variant				ENSP00000497121.1
C10orf67	ENST00000376501.7	n.466-7170G>T		intron_variant		5		ENSP00000490237.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4748857; hg19: chr10-23599558;