rs8047014

Variant names:

• chr16-69101146-C-A
• rs8047014
• XM_047434045.1:c.-123-4519C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-69101146-C-A
• chr16-69101146-C-G
• chr16-69101146-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 21 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88520 AN: 151728 Hom.: 26012 Cov.: 31

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.: 31 AF XY: 0.580 AC XY: 43033 AN XY: 74200

African (AFR) AF: 0.596 AC: 24689 AN: 41406

American (AMR) AF: 0.627 AC: 9545 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2207 AN: 3464

East Asian (EAS) AF: 0.672 AC: 3462 AN: 5152

South Asian (SAS) AF: 0.520 AC: 2504 AN: 4820

European-Finnish (FIN) AF: 0.482 AC: 5083 AN: 10548

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.579 AC: 39321 AN: 67916

Other (OTH) AF: 0.588 AC: 1240 AN: 2110

Alfa AF: 0.585 Hom.: 86235

Bravo AF: 0.595

Asia WGS AF: 0.582 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.92
DANN	Benign	0.72
PhyloP100		-0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8047014; hg19: chr16-69135049;