Variant rs2071204 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000336307.6(HYAL3):c.985-41A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0431 in 1,611,666 control chromosomes in the GnomAD database, including 12,981 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 0.10 ( 2267 hom., cov: 33)

Exomes 𝑓: 0.037 ( 10714 hom. )

Consequence

HYAL3
ENST00000336307.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.260

Variant links:

Genes affected

HYAL3 (HGNC:5322): (hyaluronidase 3) This gene encodes a member of the hyaluronidase family. Hyaluronidases are endoglycosidase enzymes that degrade hyaluronan, one of the major glycosaminoglycans of the extracellular matrix. The regulated turnover of hyaluronan plays a critical role in many biological processes including cell proliferation, migration and differentiation. The encoded protein may also play an important role in sperm function. This gene is one of several related genes in a region of chromosome 3p21.3 associated with tumor suppression, and the expression of specific transcript variants may be indicative of tumor status. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and some isoforms may lack hyaluronidase activity. This gene overlaps and is on the same strand as N-acetyltransferase 6 (GCN5-related), and some transcripts of each gene share a portion of the first exon. [provided by RefSeq, Jan 2011]

HYAL3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HYAL3	NM_003549.4 linkuse as main transcript	c.985-41A>G		intron_variant		ENST00000336307.6	NP_003540.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HYAL3	ENST00000336307.6 linkuse as main transcript	c.985-41A>G		intron_variant		1	NM_003549.4	ENSP00000337425	P1	O43820-1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15713

AN:

152142

Hom.:

2265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.0211

Gnomad FIN

AF:

0.0468

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00359

Gnomad OTH

AF:

0.0865

GnomAD3 exomes

AF:

0.122

AC:

30393

AN:

250048

Hom.:

7026

AF XY:

0.0990

AC XY:

13376

AN XY:

135154

show subpopulations

Gnomad AFR exome

AF:

0.177

Gnomad AMR exome

AF:

0.412

Gnomad ASJ exome

AF:

0.00332

Gnomad EAS exome

AF:

0.614

Gnomad SAS exome

AF:

0.00894

Gnomad FIN exome

AF:

0.0446

Gnomad NFE exome

AF:

0.00352

Gnomad OTH exome

AF:

0.0676

GnomAD4 exome

AF:

0.0368

AC:

53716

AN:

1459406

Hom.:

10714

Cov.:

AF XY:

0.0333

AC XY:

24171

AN XY:

725636

show subpopulations

Gnomad4 AFR exome

AF:

0.193

Gnomad4 AMR exome

AF:

0.389

Gnomad4 ASJ exome

AF:

0.00426

Gnomad4 EAS exome

AF:

0.535

Gnomad4 SAS exome

AF:

0.0102

Gnomad4 FIN exome

AF:

0.0440

Gnomad4 NFE exome

AF:

0.00173

Gnomad4 OTH exome

AF:

0.0565

GnomAD4 genome

AF:

0.103

AC:

15743

AN:

152260

Hom.:

2267

Cov.:

AF XY:

0.110

AC XY:

8185

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.181

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.599

Gnomad4 SAS

AF:

0.0209

Gnomad4 FIN

AF:

0.0468

Gnomad4 NFE

AF:

0.00359

Gnomad4 OTH

AF:

0.0870

Alfa

AF:

0.0738

Hom.:

354

Bravo

AF:

0.129

Asia WGS

AF:

0.206

AC:

713

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.63

DANN

Benign

0.41

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over