Genetic Variant HACL1:c.*8C>T (chr3-15560857-G-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_012260.4(HACL1):c.*8C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,593,954 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0019 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0022 ( 7 hom. )

Consequence

HACL1
NM_012260.4 3_prime_UTR

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0110

Variant links:

Genes affected

HACL1 (HGNC:17856): (2-hydroxyacyl-CoA lyase 1) Enables several functions, including 2-hydroxy-3-methylhexadecanoyl-CoA lyase activity; ATP binding activity; and cation binding activity. Involved in fatty acid alpha-oxidation; phytanic acid metabolic process; and protein targeting to peroxisome. Located in nucleoplasm and peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

HACL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 3-15560857-G-A is Benign according to our data. Variant chr3-15560857-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3038227.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HACL1	NM_012260.4 link	c.*8C>T		3_prime_UTR_variant	Exon 17 of 17	ENST00000321169.10	NP_036392.2	Q9UJ83-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HACL1	ENST00000321169 link	c.*8C>T		3_prime_UTR_variant	Exon 17 of 17	1	NM_012260.4	ENSP00000323811.5		Q9UJ83-1

Frequencies

GnomAD3 genomes

AF:

0.00186

AC:

283

AN:

152146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000676

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.00111

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00293

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00184

AC:

453

AN:

245940

Hom.:

AF XY:

0.00196

AC XY:

260

AN XY:

132950

show subpopulations

Gnomad AFR exome

AF:

0.000869

Gnomad AMR exome

AF:

0.000611

Gnomad ASJ exome

AF:

0.000101

Gnomad EAS exome

AF:

0.0000552

Gnomad SAS exome

AF:

0.00157

Gnomad FIN exome

AF:

0.00213

Gnomad NFE exome

AF:

0.00284

Gnomad OTH exome

AF:

0.00116

GnomAD4 exome

AF:

0.00224

AC:

3233

AN:

1441690

Hom.:

Cov.:

AF XY:

0.00222

AC XY:

1595

AN XY:

718038

show subpopulations

Gnomad4 AFR exome

AF:

0.000853

Gnomad4 AMR exome

AF:

0.000652

Gnomad4 ASJ exome

AF:

0.0000771

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.00164

Gnomad4 FIN exome

AF:

0.00262

Gnomad4 NFE exome

AF:

0.00254

Gnomad4 OTH exome

AF:

0.00179

GnomAD4 genome

AF:

0.00185

AC:

282

AN:

152264

Hom.:

Cov.:

AF XY:

0.00180

AC XY:

134

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.000674

Gnomad4 AMR

AF:

0.00111

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.00291

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00228

Hom.:

Bravo

AF:

0.00156

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

HACL1-related disorder

Benign:1

Mar 18, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.7

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over