rs1504058

chr3-1048918-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 0.349 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;