4-64279754-AT-A

Position:

• chr4-64279754-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.272

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]

ACMG classification

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
TECRL	NM_001010874.5	c.*317del		3_prime_UTR_variant	12/12	ENST00000381210.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TECRL	ENST00000381210.8	c.*317del		3_prime_UTR_variant	12/12	1	NM_001010874.5	P1
TECRL	ENST00000507440.5	c.964+1286del		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.966 AC: 146119 AN: 151196 Hom.: 70620 Cov.: 0

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

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

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs11303004; hg19: chr4-65145472;