rs4588572

Variant names:

• chr5-78335810-A-G
• rs4588572

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 0.194 in 152,214 control chromosomes in the GnomAD database, including 3,556 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 0.19 (3556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.337 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: 0.194 AC: 29550 AN: 152096 Hom.: 3541 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.194 AC: 29588 AN: 152214 Hom.: 3556 Cov.: 32 AF XY: 0.197 AC XY: 14639 AN XY: 74426

African (AFR) AF: 0.0893 AC: 3710 AN: 41552

American (AMR) AF: 0.345 AC: 5267 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3470

East Asian (EAS) AF: 0.0696 AC: 361 AN: 5186

South Asian (SAS) AF: 0.164 AC: 792 AN: 4828

European-Finnish (FIN) AF: 0.242 AC: 2565 AN: 10584

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15096 AN: 68010

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.220 Hom.: 6413

Bravo AF: 0.202

Asia WGS AF: 0.142 AC: 493 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.78
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4588572; hg19: chr5-77631634;