rs1504058

Variant names:

• chr3-1048918-A-G
• rs1504058

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.275 AC: 11415 AN: 41476

American (AMR) AF: 0.269 AC: 4079 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1136 AN: 3460

East Asian (EAS) AF: 0.137 AC: 711 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1044 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4578 AN: 10586

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28669 AN: 67582

Other (OTH) AF: 0.334 AC: 703 AN: 2104

Alfa AF: 0.393 Hom.: 14563

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1504058; hg19: chr3-1090602;