chr10-23310629-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001371909.1(C10orf67):​c.547-7170G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,054 control chromosomes in the GnomAD database, including 14,425 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 0.39 (14425 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

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>A		intron	N/A	NP_001358838.1	A0A6E2AE84
	C10orf67	NM_001365862.2		c.550-7170G>A		intron	N/A	NP_001352791.1	Q8IYJ2-1
	C10orf67	NM_001351306.2		c.550-7170G>A		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>A		intron	N/A	ENSP00000490528.2	A0A6E2AE84
	C10orf67	ENST00000953961.1		c.547-7170G>A		intron	N/A	ENSP00000624020.1
	C10orf67	ENST00000892141.1		c.547-7170G>A		intron	N/A	ENSP00000562200.1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58968 AN: 151936 Hom.: 14388 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.388 AC: 59052 AN: 152054 Hom.: 14425 Cov.: 32 AF XY: 0.390 AC XY: 29027 AN XY: 74334

African (AFR) AF: 0.644 AC: 26708 AN: 41474

American (AMR) AF: 0.453 AC: 6919 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1215 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3803 AN: 5150

South Asian (SAS) AF: 0.397 AC: 1916 AN: 4824

European-Finnish (FIN) AF: 0.209 AC: 2211 AN: 10578

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15116 AN: 67964

Other (OTH) AF: 0.394 AC: 832 AN: 2110

Alfa AF: 0.323 Hom.: 1352

Bravo AF: 0.425

Asia WGS AF: 0.530 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.57
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;