rs725859

Positions:

• chr7-123784529-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047420093.1(HYAL4):​c.-1823-2805G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,244 control chromosomes in the GnomAD database, including 417 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 0.066 (417 hom., cov: 32)
• Consequence: HYAL4 XM_047420093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

HYAL4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HYAL4	XM_047420093.1	c.-1823-2805G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10025 AN: 152124 Hom.: 417 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0658 AC: 10022 AN: 152244 Hom.: 417 Cov.: 32 AF XY: 0.0684 AC XY: 5091 AN XY: 74432

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.0566

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0678 Hom.: 75

Bravo AF: 0.0604

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725859; hg19: chr7-123424583;