Variant chr4-64280237-T-G 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 NM_001010874.5(TECRL):c.965-38A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 151,912 control chromosomes in the GnomAD database, including 71,139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.97 ( 71139 hom., cov: 31)

Exomes 𝑓: 0.98 ( 598030 hom. )

Failed GnomAD Quality Control

Consequence

TECRL
NM_001010874.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0860

Variant links:

Genes affected

TECRL (HGNC:27365): (trans-2,3-enoyl-CoA reductase like) The protein encoded by this gene contains a ubiquitin-like domain in the N-terminal region, three transmembrane segments and a C-terminal 3-oxo-5-alpha steroid 4-dehydrogenase domain. The protein belongs to the steroid 5-alpha reductase family. Mutations in this gene result in ventricular tachycardia, catecholaminergic polymorphic, 3. [provided by RefSeq, Apr 2017]

TECRL 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=-0.84).

BP6

Variant 4-64280237-T-G is Benign according to our data. Variant chr4-64280237-T-G is described in ClinVar as [Benign]. Clinvar id is 1225599.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TECRL	NM_001010874.5 linkuse as main transcript	c.965-38A>C		intron_variant		ENST00000381210.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
TECRL	ENST00000381210.8 linkuse as main transcript	c.965-38A>C	intron_variant	1	NM_001010874.5	P1
TECRL	ENST00000511997.1 linkuse as main transcript	c.64-38A>C	intron_variant	1
TECRL	ENST00000507440.5 linkuse as main transcript	c.964+804A>C	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.968

AC:

146899

AN:

151796

Hom.:

71104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.946

Gnomad AMI

AF:

0.916

Gnomad AMR

AF:

0.978

Gnomad ASJ

AF:

0.965

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.989

Gnomad FIN

AF:

0.988

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.972

Gnomad OTH

AF:

0.965

GnomAD3 exomes

AF:

0.978

AC:

153547

AN:

156962

Hom.:

75112

AF XY:

0.979

AC XY:

85785

AN XY:

87636

show subpopulations

Gnomad AFR exome

AF:

0.950

Gnomad AMR exome

AF:

0.986

Gnomad ASJ exome

AF:

0.971

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.989

Gnomad FIN exome

AF:

0.984

Gnomad NFE exome

AF:

0.974

Gnomad OTH exome

AF:

0.975

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.975

AC:

1226350

AN:

1257562

Hom.:

598030

Cov.:

AF XY:

0.975

AC XY:

606963

AN XY:

622242

show subpopulations

Gnomad4 AFR exome

AF:

0.947

Gnomad4 AMR exome

AF:

0.983

Gnomad4 ASJ exome

AF:

0.967

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.988

Gnomad4 FIN exome

AF:

0.984

Gnomad4 NFE exome

AF:

0.974

Gnomad4 OTH exome

AF:

0.974

GnomAD4 genome

AF:

0.968

AC:

146992

AN:

151912

Hom.:

71139

Cov.:

AF XY:

0.968

AC XY:

71872

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.946

Gnomad4 AMR

AF:

0.978

Gnomad4 ASJ

AF:

0.965

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.989

Gnomad4 FIN

AF:

0.988

Gnomad4 NFE

AF:

0.972

Gnomad4 OTH

AF:

0.965

Alfa

AF:

0.968

Hom.:

9737

Bravo

AF:

0.966

Asia WGS

AF:

0.986

AC:

3369

AN:

3418

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 04, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.9

DANN

Benign

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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