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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAS3	XM_047434045.1	c.-123-4519C>A		intron_variant	Intron 2 of 5		XP_047290001.1
HAS3	XM_047434046.1	c.-124+1480C>A		intron_variant	Intron 2 of 5		XP_047290002.1
HAS3	XM_047434047.1	c.-104+1480C>A		intron_variant	Intron 2 of 5		XP_047290003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;