rs4588572

Positions:

• chr5-78335810-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 0.194 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.78335810A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0893

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0696

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.192

Alfa AF: 0.220 Hom.: 4988

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4588572; hg19: chr5-77631634;