10-23310629-C-T

Position:

• chr10-23310629-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

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

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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.394

Alfa AF: 0.310 Hom.: 1188

Bravo AF: 0.425

Asia WGS AF: 0.530 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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;