rs11241507

chr5-119523259-A-Gchr5-119523259-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000414.4(HSD17B4):c.1504-1957A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,062 control chromosomes in the GnomAD database, including 7,236 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7236 hom., cov: 32)
• Consequence: HSD17B4 NM_000414.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B4	NM_000414.4	c.1504-1957A>G		intron_variant		ENST00000510025.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B4	ENST00000510025.7	c.1504-1957A>G		intron_variant		2	NM_000414.4	P1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42575 AN: 151944 Hom.: 7229 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.306

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42601 AN: 152062 Hom.: 7236 Cov.: 32 AF XY: 0.286 AC XY: 21225 AN XY: 74324

Gnomad4 AFR AF: 0.0909

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.304

Alfa AF: 0.259 Hom.: 1170

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.8
Dann	Benign	0.79

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

Other links and lift over

dbSNP: rs11241507; hg19: chr5-118858954;