rs4731120

chr7-123771169-A-C

Variant summary

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

The XM_047420093.1(HYAL4):c.-1824+7433A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.066 in 152,236 control chromosomes in the GnomAD database, including 421 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 (421 hom., cov: 32)
• Consequence: HYAL4 XM_047420093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

HYAL4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HYAL4	XM_047420093.1	c.-1824+7433A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 10045 AN: 152118 Hom.: 421 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0660 AC: 10042 AN: 152236 Hom.: 421 Cov.: 32 AF XY: 0.0685 AC XY: 5098 AN XY: 74440

Gnomad4 AFR AF: 0.0255

Gnomad4 AMR AF: 0.0555

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0506

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0789

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0781 Hom.: 636

Bravo AF: 0.0605

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	-0.99
Cadd	Benign	0.32
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731120; hg19: chr7-123411223;