Variant rs8047014 details in Genebe, Genetics Data Aggregator

Variant summary

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

The XM_047434045.1(HAS3):c.-123-4519C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,844 control chromosomes in the GnomAD database, including 26,031 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 0.58 ( 26031 hom., cov: 31)

Consequence

HAS3
XM_047434045.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.308

Variant links:

Genes affected

HAS3 (HGNC:4820): (hyaluronan synthase 3) The protein encoded by this gene is involved in the synthesis of the unbranched glycosaminoglycan hyaluronan, or hyaluronic acid, which is a major constituent of the extracellular matrix. This gene is a member of the NODC/HAS gene family. Compared to the proteins encoded by other members of this gene family, this protein appears to be more of a regulator of hyaluronan synthesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]

HAS3 links:

(HGNC:):

links:

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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 = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
HAS3	XM_047434045.1 linkuse as main transcript	c.-123-4519C>A	intron_variant	XP_047290001.1
HAS3	XM_047434046.1 linkuse as main transcript	c.-124+1480C>A	intron_variant	XP_047290002.1
HAS3	XM_047434047.1 linkuse as main transcript	c.-104+1480C>A	intron_variant	XP_047290003.1
	use as main transcript	n.69101146C>A	intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88520

AN:

151728

Hom.:

26012

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.627

Gnomad ASJ

AF:

0.637

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.518

Gnomad FIN

AF:

0.482

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.579

Gnomad OTH

AF:

0.594

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

GnomAD4 genome

AF:

0.583

AC:

88575

AN:

151844

Hom.:

26031

Cov.:

AF XY:

0.580

AC XY:

43033

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.596

Gnomad4 AMR

AF:

0.627

Gnomad4 ASJ

AF:

0.637

Gnomad4 EAS

AF:

0.672

Gnomad4 SAS

AF:

0.520

Gnomad4 FIN

AF:

0.482

Gnomad4 NFE

AF:

0.579

Gnomad4 OTH

AF:

0.588

Alfa

AF:

0.583

Hom.:

56842

Bravo

AF:

0.595

Asia WGS

AF:

0.582

AC:

2026

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

0.92

DANN

Benign

0.72

Splicing

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