Variant chr5-41870573-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000510509.1(OXCT1-AS1):n.356T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 594,638 control chromosomes in the GnomAD database, including 14,979 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3823 hom., cov: 33)

Exomes 𝑓: 0.22 ( 11156 hom. )

Consequence

OXCT1-AS1
ENST00000510509.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.384

Variant links:

Genes affected

OXCT1-AS1 (HGNC:):

OXCT1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 5-41870573-T-C is Benign according to our data. Variant chr5-41870573-T-C is described in ClinVar as [Benign]. Clinvar id is 353674.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
OXCT1-AS1	NR_046635.1 linkuse as main transcript	n.255+191T>C	intron_variant
LOC102723752	XR_007058750.1 linkuse as main transcript	n.41+1540T>C	intron_variant
LOC102723752	XR_427695.4 linkuse as main transcript	n.80+1501T>C	intron_variant
LOC102723752	XR_925956.4 linkuse as main transcript	n.6415+971T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
OXCT1-AS1	ENST00000510509.1 linkuse as main transcript	n.356T>C	non_coding_transcript_exon_variant	2/2	3
OXCT1-AS1	ENST00000654321.1 linkuse as main transcript	n.549T>C	non_coding_transcript_exon_variant	2/2
OXCT1-AS1	ENST00000508458.2 linkuse as main transcript	n.255+191T>C	intron_variant		3
ENSG00000286164	ENST00000651810.1 linkuse as main transcript	n.98+1501T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33522

AN:

152080

Hom.:

3808

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.440

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.0325

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.236

GnomAD4 exome

AF:

0.217

AC:

95964

AN:

442440

Hom.:

11156

Cov.:

AF XY:

0.220

AC XY:

52050

AN XY:

236082

show subpopulations

Gnomad4 AFR exome

AF:

0.219

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.260

Gnomad4 EAS exome

AF:

0.0401

Gnomad4 SAS exome

AF:

0.266

Gnomad4 FIN exome

AF:

0.241

Gnomad4 NFE exome

AF:

0.218

Gnomad4 OTH exome

AF:

0.227

GnomAD4 genome

AF:

0.221

AC:

33582

AN:

152198

Hom.:

3823

Cov.:

AF XY:

0.225

AC XY:

16734

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.0325

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.236

Alfa

AF:

0.220

Hom.:

810

Bravo

AF:

0.218

Asia WGS

AF:

0.143

AC:

497

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 20, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Succinyl-CoA acetoacetate transferase deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.7

DANN

Benign

0.43

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