rs1504058

Variant names:

• chr3-1048918-A-G
• rs1504058

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 0.349 in 151,570 control chromosomes in the GnomAD database, including 9,729 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 0.35 (9729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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: 0.349 AC: 52911 AN: 151452 Hom.: 9730 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.349 AC: 52919 AN: 151570 Hom.: 9729 Cov.: 32 AF XY: 0.345 AC XY: 25597 AN XY: 74096

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.334

Alfa AF: 0.394 Hom.: 12088

Bravo AF: 0.336

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504058; hg19: chr3-1090602;