Variant 1-151847242-AGGAGGCAGGAGGCAGGCAGG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_182578.4(THEM5):c.*109_*128del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0062 ( 21 hom., cov: 0)

Exomes 𝑓: 0.0028 ( 30 hom. )

Failed GnomAD Quality Control

Consequence

THEM5
NM_182578.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

THEM5 (HGNC:26755): (thioesterase superfamily member 5) Enables palmitoyl-CoA hydrolase activity. Involved in long-chain fatty-acyl-CoA metabolic process. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

THEM5 links:

C2CD4D-AS1 (HGNC:54045): (C2CD4D and THEM5 antisense RNA 1)

C2CD4D-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 1-151847242-AGGAGGCAGGAGGCAGGCAGG-A is Benign according to our data. Variant chr1-151847242-AGGAGGCAGGAGGCAGGCAGG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2639182.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 21 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
THEM5	NM_182578.4 linkuse as main transcript	c.109_128del		3_prime_UTR_variant	6/6	ENST00000368817.10	NP_872384.2
C2CD4D-AS1	NR_024237.2 linkuse as main transcript	n.1031-2954_1031-2935del		intron_variant, non_coding_transcript_variant
THEM5	XM_011509421.2 linkuse as main transcript	c.728_747del	p.Pro243LeufsTer31	frameshift_variant	5/5		XP_011507723.1
C2CD4D-AS1	NR_152846.1 linkuse as main transcript	n.951-2954_951-2935del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
THEM5	ENST00000368817.10 linkuse as main transcript	c.109_128del	3_prime_UTR_variant	6/6	1	NM_182578.4	ENSP00000357807	P1
C2CD4D-AS1	ENST00000434182.1 linkuse as main transcript	n.354-2954_354-2935del	intron_variant, non_coding_transcript_variant		5
THEM5	ENST00000453881.2 linkuse as main transcript		downstream_gene_variant		4		ENSP00000406809

Frequencies

GnomAD3 genomes

AF:

0.00598

AC:

AN:

10366

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00173

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0159

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.00758

Gnomad SAS

AF:

0.0185

Gnomad FIN

AF:

0.0372

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0128

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000392

AC:

AN:

112138

Hom.:

AF XY:

0.000382

AC XY:

AN XY:

60242

show subpopulations

Gnomad AFR exome

AF:

0.000882

Gnomad AMR exome

AF:

0.000299

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00103

Gnomad SAS exome

AF:

0.000386

Gnomad FIN exome

AF:

0.000572

Gnomad NFE exome

AF:

0.000248

Gnomad OTH exome

AF:

0.000602

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00278

AC:

254

AN:

91220

Hom.:

AF XY:

0.00282

AC XY:

138

AN XY:

48862

show subpopulations

Gnomad4 AFR exome

AF:

0.00266

Gnomad4 AMR exome

AF:

0.000619

Gnomad4 ASJ exome

AF:

0.000896

Gnomad4 EAS exome

AF:

0.0383

Gnomad4 SAS exome

AF:

0.00175

Gnomad4 FIN exome

AF:

0.00423

Gnomad4 NFE exome

AF:

0.00334

Gnomad4 OTH exome

AF:

0.00316

GnomAD4 genome

AF:

0.00616

AC:

AN:

10386

Hom.:

Cov.:

AF XY:

0.00415

AC XY:

AN XY:

5058

show subpopulations

Gnomad4 AFR

AF:

0.00201

Gnomad4 AMR

AF:

0.0159

Gnomad4 ASJ

AF:

0.0294

Gnomad4 EAS

AF:

0.00781

Gnomad4 SAS

AF:

0.0190

Gnomad4 FIN

AF:

0.0372

Gnomad4 NFE

AF:

0.0128

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0128

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

THEM5: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over