rs4748857

Variant names:

• chr10-23310629-C-A
• rs4748857
• NM_001371909.1:c.547-7170G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-23310629-C-A
• chr10-23310629-C-G
• chr10-23310629-C-T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf67	NM_001371909.1	MANE Select	c.547-7170G>T		intron	N/A	NP_001358838.1	A0A6E2AE84
	C10orf67	NM_001365862.2		c.550-7170G>T		intron	N/A	NP_001352791.1	Q8IYJ2-1
	C10orf67	NM_001351306.2		c.550-7170G>T		intron	N/A	NP_001338235.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf67	ENST00000636213.3	TSL:5 MANE Select	c.547-7170G>T		intron	N/A	ENSP00000490528.2	A0A6E2AE84
	C10orf67	ENST00000953961.1		c.547-7170G>T		intron	N/A	ENSP00000624020.1
	C10orf67	ENST00000892141.1		c.547-7170G>T		intron	N/A	ENSP00000562200.1

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs4748857; hg19: chr10-23599558;