rs8047014

chr16-69101146-C-Achr16-69101146-C-Gchr16-69101146-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

HAS3 (HGNC:):

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	UniProt
HAS3	XM_047434045.1	c.-123-4519C>A		intron_variant
HAS3	XM_047434046.1	c.-124+1480C>A		intron_variant
HAS3	XM_047434047.1	c.-104+1480C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

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

Other links and lift over

dbSNP: rs8047014; hg19: chr16-69135049;