rs1521003

Variant names:

• chr5-23704487-T-A
• rs1521003

Your query was ambiguous. Multiple possible variants found:

• chr5-23704487-T-A
• chr5-23704487-T-C
• chr5-23704487-T-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 0.916 in 152,022 control chromosomes in the GnomAD database, including 63,941 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 0.92 (63941 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.917 AC: 139223 AN: 151904 Hom.: 63902 Cov.: 33

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.916 AC: 139321 AN: 152022 Hom.: 63941 Cov.: 33 AF XY: 0.916 AC XY: 68114 AN XY: 74330

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.934

Alfa AF: 0.912 Hom.: 7706

Bravo AF: 0.921

Asia WGS AF: 0.955 AC: 3315 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1521003; hg19: chr5-23704596;