1-151847242-AGGAGGCAGGAGGCAGGCAGG-A

Variant names:

• chr1-151847242-AGGAGGCAGGAGGCAGGCAGG-A
• NM_182578.4:c.*109_*128delCCTGCCTGCCTCCTGCCTCC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_182578.4(THEM5):​c.*109_*128delCCTGCCTGCCTCCTGCCTCC 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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.40

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]

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

ACMG classification

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 rank	MANE	Protein	UniProt
THEM5	NM_182578.4	c.*109_*128delCCTGCCTGCCTCCTGCCTCC		3_prime_UTR_variant	Exon 6 of 6	ENST00000368817.10	NP_872384.2
THEM5	XM_011509421.2	c.728_747delCCTGCCTGCCTCCTGCCTCC	p.Pro243LeufsTer31	frameshift_variant	Exon 5 of 5		XP_011507723.1
C2CD4D-AS1	NR_024237.2	n.1031-2954_1031-2935delCAGGGGAGGCAGGAGGCAGG		intron_variant	Intron 4 of 4
C2CD4D-AS1	NR_152846.1	n.951-2954_951-2935delCAGGGGAGGCAGGAGGCAGG		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THEM5	ENST00000368817	c.*109_*128delCCTGCCTGCCTCCTGCCTCC		3_prime_UTR_variant	Exon 6 of 6	1	NM_182578.4	ENSP00000357807.4
C2CD4D-AS1	ENST00000434182.1	n.354-2954_354-2935delCAGGGGAGGCAGGAGGCAGG		intron_variant	Intron 2 of 2	5
THEM5	ENST00000453881.2	c.*20_*39delCCTGCCTGCCTCCTGCCTCC		downstream_gene_variant		4		ENSP00000406809.2

Frequencies

GnomAD3 genomes AF: 0.00598 AC: 62 AN: 10366 Hom.: 20 Cov.: 0

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: 44 AN: 112138 Hom.: 18 AF XY: 0.000382 AC XY: 23 AN XY: 60242

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.: 30 AF XY: 0.00282 AC XY: 138 AN XY: 48862

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: 64 AN: 10386 Hom.: 21 Cov.: 0 AF XY: 0.00415 AC XY: 21 AN XY: 5058

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.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

THEM5: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-151819718;