rs4704559

chr5-79517086-A-G

Variant summary

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

The variant allele was found at a frequency of 0.152 in 152,070 control chromosomes in the GnomAD database, including 2,259 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 0.15 (2259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23023 AN: 151952 Hom.: 2257 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.152 AC: 23050 AN: 152070 Hom.: 2259 Cov.: 32 AF XY: 0.150 AC XY: 11188 AN XY: 74366

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0741

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.0923

Gnomad4 OTH AF: 0.149

Alfa AF: 0.107 Hom.: 994

Bravo AF: 0.167

Asia WGS AF: 0.0980 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	12
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4704559; hg19: chr5-78812909;