rs4704559

Variant names:

• chr5-79517086-A-G
• rs4704559

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.263 AC: 10899 AN: 41442

American (AMR) AF: 0.212 AC: 3244 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3470

East Asian (EAS) AF: 0.0741 AC: 384 AN: 5182

South Asian (SAS) AF: 0.0980 AC: 472 AN: 4816

European-Finnish (FIN) AF: 0.0944 AC: 999 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0923 AC: 6277 AN: 67980

Other (OTH) AF: 0.149 AC: 314 AN: 2108

Alfa AF: 0.114 Hom.: 3309

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4704559; hg19: chr5-78812909;