4-64280982-A-G

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+59T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 1,280,848 control chromosomes in the GnomAD database, including 569,650 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.85 ( 57579 hom., cov: 32)
Exomes 𝑓: 0.95 ( 512071 hom. )

Consequence

TECRL
NM_001010874.5 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -0.287
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]

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=-0.88).
BP6
Variant 4-64280982-A-G is Benign according to our data. Variant chr4-64280982-A-G is described in ClinVar as [Benign]. Clinvar id is 1221036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TECRLNM_001010874.5 linkuse as main transcriptc.964+59T>C intron_variant ENST00000381210.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TECRLENST00000381210.8 linkuse as main transcriptc.964+59T>C intron_variant 1 NM_001010874.5 P1
TECRLENST00000511997.1 linkuse as main transcriptc.63+492T>C intron_variant 1
TECRLENST00000507440.5 linkuse as main transcriptc.964+59T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.855
AC:
129842
AN:
151888
Hom.:
57580
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.589
Gnomad AMI
AF:
0.917
Gnomad AMR
AF:
0.923
Gnomad ASJ
AF:
0.932
Gnomad EAS
AF:
0.997
Gnomad SAS
AF:
0.968
Gnomad FIN
AF:
0.986
Gnomad MID
AF:
0.930
Gnomad NFE
AF:
0.956
Gnomad OTH
AF:
0.870
GnomAD4 exome
AF:
0.950
AC:
1072867
AN:
1128842
Hom.:
512071
AF XY:
0.952
AC XY:
543941
AN XY:
571074
show subpopulations
Gnomad4 AFR exome
AF:
0.572
Gnomad4 AMR exome
AF:
0.953
Gnomad4 ASJ exome
AF:
0.932
Gnomad4 EAS exome
AF:
0.999
Gnomad4 SAS exome
AF:
0.972
Gnomad4 FIN exome
AF:
0.981
Gnomad4 NFE exome
AF:
0.958
Gnomad4 OTH exome
AF:
0.930
GnomAD4 genome
AF:
0.854
AC:
129870
AN:
152006
Hom.:
57579
Cov.:
32
AF XY:
0.860
AC XY:
63873
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.588
Gnomad4 AMR
AF:
0.924
Gnomad4 ASJ
AF:
0.932
Gnomad4 EAS
AF:
0.997
Gnomad4 SAS
AF:
0.968
Gnomad4 FIN
AF:
0.986
Gnomad4 NFE
AF:
0.956
Gnomad4 OTH
AF:
0.869
Alfa
AF:
0.891
Hom.:
5361
Bravo
AF:
0.838
Asia WGS
AF:
0.948
AC:
3294
AN:
3476

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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxSep 04, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.2
DANN
Benign
0.57

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.

Other links and lift over

dbSNP: rs10012755; hg19: chr4-65146700; API