4-64280248-T-TAA

Variant summary

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

The NM_001010874.5(TECRL):c.965-50_965-49insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.97 (71174 hom., cov: 0)
  • Exomes 𝑓: 0.97 (569103 hom.)
• Consequence: TECRL NM_001010874.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.11

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 4-64280248-T-TAA is Benign according to our data. Variant chr4-64280248-T-TAA is described in ClinVar as [Benign]. Clinvar id is 1294827.Status of the report is criteria_provided_single_submitter, 1 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	c.965-50_965-49insTT		intron_variant		ENST00000381210.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TECRL	ENST00000381210.8	c.965-50_965-49insTT		intron_variant		1	NM_001010874.5	P1
TECRL	ENST00000511997.1	c.64-50_64-49insTT		intron_variant		1
TECRL	ENST00000507440.5	c.964+792_964+793insTT		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.968 AC: 146970 AN: 151866 Hom.: 71139 Cov.: 0

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.978

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: 0.965

GnomAD3 exomes AF: 0.978 AC: 131364 AN: 134378 Hom.: 64221 AF XY: 0.978 AC XY: 73096 AN XY: 74730

Gnomad AFR exome AF: 0.948

Gnomad AMR exome AF: 0.985

Gnomad ASJ exome AF: 0.967

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: 0.974 AC: 1167551 AN: 1198170 Hom.: 569103 Cov.: 12 AF XY: 0.975 AC XY: 576971 AN XY: 591956

Gnomad4 AFR exome AF: 0.945

Gnomad4 AMR exome AF: 0.982

Gnomad4 ASJ exome AF: 0.966

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.988

Gnomad4 FIN exome AF: 0.984

Gnomad4 NFE exome AF: 0.973

Gnomad4 OTH exome AF: 0.973

GnomAD4 genome AF: 0.968 AC: 147063 AN: 151982 Hom.: 71174 Cov.: 0 AF XY: 0.968 AC XY: 71912 AN XY: 74278

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.978

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: 0.965

Alfa AF: 0.968 Hom.: 9427

Bravo AF: 0.966

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

Mar 29, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5858871; hg19: chr4-65145966;