Variant chr5-41870550-C-T 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.333C>T 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 0.0404 in 624,282 control chromosomes in the GnomAD database, including 670 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.036 ( 148 hom., cov: 33)

Exomes 𝑓: 0.042 ( 522 hom. )

Consequence

OXCT1-AS1
ENST00000510509.1 non_coding_transcript_exon

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.395

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=-0.64).

BP6

Variant 5-41870550-C-T is Benign according to our data. Variant chr5-41870550-C-T is described in ClinVar as [Benign]. Clinvar id is 353673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
OXCT1-AS1	NR_046635.1 linkuse as main transcript	n.255+168C>T	intron_variant
LOC102723752	XR_007058750.1 linkuse as main transcript	n.41+1517C>T	intron_variant
LOC102723752	XR_427695.4 linkuse as main transcript	n.80+1478C>T	intron_variant
LOC102723752	XR_925956.4 linkuse as main transcript	n.6415+948C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
OXCT1-AS1	ENST00000510509.1 linkuse as main transcript	n.333C>T	non_coding_transcript_exon_variant	2/2	3
OXCT1-AS1	ENST00000654321.1 linkuse as main transcript	n.526C>T	non_coding_transcript_exon_variant	2/2
OXCT1-AS1	ENST00000508458.2 linkuse as main transcript	n.255+168C>T	intron_variant		3
ENSG00000286164	ENST00000651810.1 linkuse as main transcript	n.98+1478C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0359

AC:

5460

AN:

152174

Hom.:

148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0111

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.0266

Gnomad ASJ

AF:

0.0392

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0180

Gnomad FIN

AF:

0.0497

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0537

Gnomad OTH

AF:

0.0398

GnomAD4 exome

AF:

0.0419

AC:

19771

AN:

471990

Hom.:

522

Cov.:

AF XY:

0.0403

AC XY:

10163

AN XY:

252236

show subpopulations

Gnomad4 AFR exome

AF:

0.0116

Gnomad4 AMR exome

AF:

0.0246

Gnomad4 ASJ exome

AF:

0.0372

Gnomad4 EAS exome

AF:

0.0000325

Gnomad4 SAS exome

AF:

0.0164

Gnomad4 FIN exome

AF:

0.0575

Gnomad4 NFE exome

AF:

0.0527

Gnomad4 OTH exome

AF:

0.0436

GnomAD4 genome

AF:

0.0359

AC:

5461

AN:

152292

Hom.:

148

Cov.:

AF XY:

0.0340

AC XY:

2536

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.0111

Gnomad4 AMR

AF:

0.0266

Gnomad4 ASJ

AF:

0.0392

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0184

Gnomad4 FIN

AF:

0.0497

Gnomad4 NFE

AF:

0.0537

Gnomad4 OTH

AF:

0.0393

Alfa

AF:

0.0421

Hom.:

Bravo

AF:

0.0338

Asia WGS

AF:

0.00693

AC:

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	Nov 12, 2018	- -
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

-0.64

CADD

Benign

DANN

Benign

0.91

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