rs141619383

Variant names:

• chr19-14565757-C-T
• rs141619383
• NM_138501.6:c.813C>T

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_138501.6(TECR):​c.813C>T​(p.Ser271Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00567 in 1,612,056 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0048 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0058 (34 hom.)
• Consequence: TECR NM_138501.6 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.841
• Publications: 3 publications found

Genes affected

TECR (HGNC:4551): (trans-2,3-enoyl-CoA reductase) This gene encodes a multi-pass membrane protein that resides in the endoplasmic reticulum, and belongs to the steroid 5-alpha reductase family. The elongation of microsomal long and very long chain fatty acid consists of 4 sequential reactions. This protein catalyzes the final step, reducing trans-2,3-enoyl-CoA to saturated acyl-CoA. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Apr 2011]

TECR Gene-Disease associations (from GenCC):

• autosomal recessive non-syndromic intellectual disability

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• intellectual disability

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen
• intellectual disability, autosomal recessive 14

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BP6: Variant 19-14565757-C-T is Benign according to our data. Variant chr19-14565757-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 212396.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.841 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138501.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TECR	NM_138501.6	MANE Select	c.813C>T	p.Ser271Ser	synonymous	Exon 13 of 13	NP_612510.1
	TECR	NM_001321170.1		c.858C>T	p.Ser286Ser	synonymous	Exon 14 of 14	NP_001308099.1
	TECR	NR_038103.2		n.948C>T		non_coding_transcript_exon	Exon 13 of 13

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TECR	ENST00000215567.10	TSL:1 MANE Select	c.813C>T	p.Ser271Ser	synonymous	Exon 13 of 13	ENSP00000215567.4
	TECR	ENST00000596073.6	TSL:1	c.927C>T	p.Ser309Ser	synonymous	Exon 12 of 12	ENSP00000472697.2
	TECR	ENST00000601187.1	TSL:3	c.339C>T	p.Ser113Ser	synonymous	Exon 6 of 6	ENSP00000472957.1

Frequencies

GnomAD3 genomes AF: 0.00476 AC: 724 AN: 152192 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00242

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00665

Gnomad OTH AF: 0.00382

GnomAD2 exomes AF: 0.00463 AC: 1138 AN: 245598 AF XY: 0.00477

Gnomad AFR exome AF: 0.000894

Gnomad AMR exome AF: 0.00122

Gnomad ASJ exome AF: 0.000405

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0148

Gnomad NFE exome AF: 0.00660

Gnomad OTH exome AF: 0.00418

GnomAD4 exome AF: 0.00576 AC: 8414 AN: 1459746 Hom.: 34 Cov.: 33 AF XY: 0.00563 AC XY: 4085 AN XY: 726174

African (AFR) AF: 0.000867 AC: 29 AN: 33460

American (AMR) AF: 0.00119 AC: 53 AN: 44622

Ashkenazi Jewish (ASJ) AF: 0.000460 AC: 12 AN: 26078

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39650

South Asian (SAS) AF: 0.000720 AC: 62 AN: 86094

European-Finnish (FIN) AF: 0.0143 AC: 744 AN: 52122

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5762

European-Non Finnish (NFE) AF: 0.00655 AC: 7279 AN: 1111648

Other (OTH) AF: 0.00385 AC: 232 AN: 60310

GnomAD4 genome AF: 0.00475 AC: 724 AN: 152310 Hom.: 3 Cov.: 32 AF XY: 0.00451 AC XY: 336 AN XY: 74476

African (AFR) AF: 0.00120 AC: 50 AN: 41586

American (AMR) AF: 0.00242 AC: 37 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00207 AC: 10 AN: 4832

European-Finnish (FIN) AF: 0.0155 AC: 165 AN: 10630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00665 AC: 452 AN: 67998

Other (OTH) AF: 0.00378 AC: 8 AN: 2114

Alfa AF: 0.00575 Hom.: 1

Bravo AF: 0.00337

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Sep 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

TECR: BP4, BP7, BS2

not specified Benign:1

Sep 11, 2017

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		-0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs141619383; hg19: chr19-14676569; COSMIC: COSV99295220; COSMIC: COSV99295220;