10-23219094-G-A

Position:

• chr10-23219094-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001371909.1(C10orf67):​c.1570+4504C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,026 control chromosomes in the GnomAD database, including 26,263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.57 (26263 hom., cov: 32)
• Consequence: C10orf67 NM_001371909.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.868

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 10-23219094-G-A is Benign according to our data. Variant chr10-23219094-G-A is described in ClinVar as [Benign]. Clinvar id is 1257978.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf67	NM_001371909.1	c.1570+4504C>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.1570+4504C>T		intron_variant		5	NM_001371909.1	ENSP00000490528.2
C10orf67	ENST00000376501.7	n.*107+4504C>T		intron_variant		5		ENSP00000490237.1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87190 AN: 151908 Hom.: 26217 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.574 AC: 87291 AN: 152026 Hom.: 26263 Cov.: 32 AF XY: 0.577 AC XY: 42867 AN XY: 74290

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.578

Alfa AF: 0.537 Hom.: 3881

Bravo AF: 0.597

Asia WGS AF: 0.708 AC: 2453 AN: 3468

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4748846; hg19: chr10-23508023;