Variant 10-23290495-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001371909.1(C10orf67):c.851-537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 151,984 control chromosomes in the GnomAD database, including 3,071 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.19 ( 3071 hom., cov: 32)

Consequence

C10orf67
NM_001371909.1 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.96

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 10-23290495-G-A is Benign according to our data. Variant chr10-23290495-G-A is described in ClinVar as [Benign]. Clinvar id is 444141.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf67	NM_001371909.1 linkuse as main transcript	c.851-537C>T		intron_variant		ENST00000636213.3	NP_001358838.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
C10orf67	ENST00000636213.3 linkuse as main transcript	c.851-537C>T	intron_variant	5	NM_001371909.1	ENSP00000490528	P1
C10orf67	ENST00000376500.5 linkuse as main transcript	c.704-537C>T	intron_variant	5		ENSP00000365683
C10orf67	ENST00000376501.7 linkuse as main transcript	c.771-537C>T	intron_variant, NMD_transcript_variant	5		ENSP00000490237

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29070

AN:

151866

Hom.:

3065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.0177

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.245

Gnomad NFE

AF:

0.174

Gnomad OTH

AF:

0.213

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

GnomAD4 genome

AF:

0.191

AC:

29098

AN:

151984

Hom.:

3071

Cov.:

AF XY:

0.191

AC XY:

14211

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.289

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.0174

Gnomad4 SAS

AF:

0.207

Gnomad4 FIN

AF:

0.140

Gnomad4 NFE

AF:

0.174

Gnomad4 OTH

AF:

0.211

Alfa

AF:

0.139

Hom.:

397

Bravo

AF:

0.204

Asia WGS

AF:

0.134

AC:

467

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Type 2 diabetes mellitus

Benign:1

Benign, no assertion criteria provided

case-control

Diabetes Molecular Genetics Section, Phoenix Epidemiology and Clinical Research Branch, National Institutes of Health

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.17

DANN

Benign

0.68

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over