chr4-64279754-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001010874.5(TECRL):​c.*317del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.97 ( 70650 hom., cov: 0)
Exomes 𝑓: 0.94 ( 307762 hom. )

Consequence

TECRL
NM_001010874.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.272
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 -10 ACMG points.

BP6
Variant 4-64279754-AT-A is Benign according to our data. Variant chr4-64279754-AT-A is described in ClinVar as [Benign]. Clinvar id is 1247451.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TECRLNM_001010874.5 linkuse as main transcriptc.*317del 3_prime_UTR_variant 12/12 ENST00000381210.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TECRLENST00000381210.8 linkuse as main transcriptc.*317del 3_prime_UTR_variant 12/121 NM_001010874.5 P1
TECRLENST00000507440.5 linkuse as main transcriptc.964+1286del intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.966
AC:
146119
AN:
151196
Hom.:
70620
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.944
Gnomad AMI
AF:
0.916
Gnomad AMR
AF:
0.977
Gnomad ASJ
AF:
0.965
Gnomad EAS
AF:
0.998
Gnomad SAS
AF:
0.987
Gnomad FIN
AF:
0.985
Gnomad MID
AF:
0.984
Gnomad NFE
AF:
0.971
Gnomad OTH
AF:
0.964
GnomAD4 exome
AF:
0.935
AC:
660746
AN:
706558
Hom.:
307762
Cov.:
0
AF XY:
0.935
AC XY:
306117
AN XY:
327290
show subpopulations
Gnomad4 AFR exome
AF:
0.903
Gnomad4 AMR exome
AF:
0.947
Gnomad4 ASJ exome
AF:
0.925
Gnomad4 EAS exome
AF:
0.954
Gnomad4 SAS exome
AF:
0.950
Gnomad4 FIN exome
AF:
0.948
Gnomad4 NFE exome
AF:
0.935
Gnomad4 OTH exome
AF:
0.936
GnomAD4 genome
AF:
0.966
AC:
146204
AN:
151304
Hom.:
70650
Cov.:
0
AF XY:
0.967
AC XY:
71455
AN XY:
73912
show subpopulations
Gnomad4 AFR
AF:
0.944
Gnomad4 AMR
AF:
0.977
Gnomad4 ASJ
AF:
0.965
Gnomad4 EAS
AF:
0.998
Gnomad4 SAS
AF:
0.987
Gnomad4 FIN
AF:
0.985
Gnomad4 NFE
AF:
0.971
Gnomad4 OTH
AF:
0.965

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 20, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs11303004; hg19: chr4-65145472; API