rs1500004

Variant names:

• chr3-46109445-G-A
• rs1500004

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 0.0628 in 152,268 control chromosomes in the GnomAD database, including 416 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 0.063 (416 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0911 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: 0.0629 AC: 9563 AN: 152150 Hom.: 416 Cov.: 33

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0628 AC: 9566 AN: 152268 Hom.: 416 Cov.: 33 AF XY: 0.0624 AC XY: 4644 AN XY: 74452

Gnomad4 AFR AF: 0.0177

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0761 Hom.: 56

Bravo AF: 0.0551

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1500004; hg19: chr3-46150937;