rs1548587

Variant names:

• chr5-138457050-A-G
• rs1548587

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 0.528 in 151,736 control chromosomes in the GnomAD database, including 21,990 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 0.53 (21990 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

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 (NFE) allele frequency at 95% confidence interval = 0.573 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: 0.527 AC: 79980 AN: 151626 Hom.: 21954 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.528 AC: 80071 AN: 151736 Hom.: 21990 Cov.: 31 AF XY: 0.526 AC XY: 39002 AN XY: 74138

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.539

Alfa AF: 0.547 Hom.: 5960

Bravo AF: 0.518

Asia WGS AF: 0.305 AC: 1060 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1548587; hg19: chr5-137792739;