rs252930

Variant names:

• chr5-5509590-A-C
• rs252930

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 0.609 in 151,970 control chromosomes in the GnomAD database, including 28,582 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 0.61 (28582 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 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: 0.609 AC: 92419 AN: 151850 Hom.: 28558 Cov.: 31

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.609 AC: 92489 AN: 151970 Hom.: 28582 Cov.: 31 AF XY: 0.604 AC XY: 44885 AN XY: 74266

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.647

Alfa AF: 0.656 Hom.: 35602

Bravo AF: 0.614

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs252930; hg19: chr5-5509703;