chr4-64280993-T-C

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

2

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]

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
TECRLNM_001010874.5 linkuse as main transcriptc.964+48A>G intron_variant ENST00000381210.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TECRLENST00000381210.8 linkuse as main transcriptc.964+48A>G intron_variant 1 NM_001010874.5 P1
TECRLENST00000511997.1 linkuse as main transcriptc.63+481A>G intron_variant 1
TECRLENST00000507440.5 linkuse as main transcriptc.964+48A>G intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.968
AC:
147051
AN:
151944
Hom.:
71181
Cov.:
32
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.:
15
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.:
32
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMar 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.

Other links and lift over

dbSNP: rs1483709; hg19: chr4-65146711; API