Variant 4-64280993-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 NM_001010874.5(TECRL):c.964+48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.975 in 1,403,786 control chromosomes in the GnomAD database, including 666,972 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.97 ( 71215 hom., cov: 32)

Exomes 𝑓: 0.98 ( 595757 hom. )

Consequence

TECRL
NM_001010874.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.42

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=-0.95).

BP6

Variant 4-64280993-T-C is Benign according to our data. Variant chr4-64280993-T-C is described in ClinVar as [Benign]. Clinvar id is 1240736.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.964+48A>G		intron_variant		ENST00000381210.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
TECRL	ENST00000381210.8 linkuse as main transcript	c.964+48A>G	intron_variant	1	NM_001010874.5	P1
TECRL	ENST00000511997.1 linkuse as main transcript	c.63+481A>G	intron_variant	1
TECRL	ENST00000507440.5 linkuse as main transcript	c.964+48A>G	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.968

AC:

147051

AN:

151944

Hom.:

71181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.946

Gnomad AMI

AF:

0.917

Gnomad AMR

AF:

0.979

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:

0.966

GnomAD3 exomes

AF:

0.978

AC:

226337

AN:

231468

Hom.:

110677

AF XY:

0.979

AC XY:

122922

AN XY:

125598

show subpopulations

Gnomad AFR exome

AF:

0.947

Gnomad AMR exome

AF:

0.986

Gnomad ASJ exome

AF:

0.970

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.988

Gnomad FIN exome

AF:

0.984

Gnomad NFE exome

AF:

0.973

Gnomad OTH exome

AF:

0.974

GnomAD4 exome

AF:

0.976

AC:

1221171

AN:

1251724

Hom.:

595757

Cov.:

AF XY:

0.976

AC XY:

614420

AN XY:

629606

show subpopulations

Gnomad4 AFR exome

AF:

0.946

Gnomad4 AMR exome

AF:

0.984

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:

147144

AN:

152062

Hom.:

71215

Cov.:

AF XY:

0.968

AC XY:

71956

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.946

Gnomad4 AMR

AF:

0.979

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:

0.966

Alfa

AF:

0.968

Hom.:

13224

Bravo

AF:

0.966

Asia WGS

AF:

0.986

AC:

3421

AN:

3470

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	Mar 29, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.64

DANN

Benign

0.40

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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