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. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.887 AC: 36817 AN: 41522

American (AMR) AF: 0.952 AC: 14540 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3301 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5161 AN: 5166

South Asian (SAS) AF: 0.967 AC: 4668 AN: 4826

European-Finnish (FIN) AF: 0.870 AC: 9220 AN: 10602

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62502 AN: 67850

Other (OTH) AF: 0.934 AC: 1973 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1521003; hg19: chr5-23704596;