Variant rs12653702 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000414.4(HSD17B4):c.714+73G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 895,662 control chromosomes in the GnomAD database, including 11,229 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 3314 hom., cov: 32)

Exomes 𝑓: 0.11 ( 7915 hom. )

Consequence

HSD17B4
NM_000414.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.02

Variant links:

Genes affected

HSD17B4 (HGNC:5213): (hydroxysteroid 17-beta dehydrogenase 4) The protein encoded by this gene is a bifunctional enzyme that is involved in the peroxisomal beta-oxidation pathway for fatty acids. It also acts as a catalyst for the formation of 3-ketoacyl-CoA intermediates from both straight-chain and 2-methyl-branched-chain fatty acids. Defects in this gene that affect the peroxisomal fatty acid beta-oxidation activity are a cause of D-bifunctional protein deficiency (DBPD). An apparent pseudogene of this gene is present on chromosome 8. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]

HSD17B4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 5-119489356-G-C is Benign according to our data. Variant chr5-119489356-G-C is described in ClinVar as [Benign]. Clinvar id is 1249115.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B4	NM_000414.4 linkuse as main transcript	c.714+73G>C		intron_variant		ENST00000510025.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B4	ENST00000510025.7 linkuse as main transcript	c.714+73G>C		intron_variant		2	NM_000414.4	P1	P51659-1

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25465

AN:

151846

Hom.:

3305

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0897

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0766

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.113

AC:

84018

AN:

743698

Hom.:

7915

AF XY:

0.111

AC XY:

44191

AN XY:

397976

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.0846

Gnomad4 EAS exome

AF:

0.452

Gnomad4 SAS exome

AF:

0.123

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.0755

Gnomad4 OTH exome

AF:

0.121

GnomAD4 genome

AF:

0.168

AC:

25497

AN:

151964

Hom.:

3314

Cov.:

AF XY:

0.170

AC XY:

12631

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.103

Gnomad4 ASJ

AF:

0.0897

Gnomad4 EAS

AF:

0.410

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.0765

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.126

Hom.:

219

Bravo

AF:

0.177

Asia WGS

AF:

0.230

AC:

799

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.1

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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