rs1533317

Variant names:

• chr4-35409009-T-C
• rs1533317

Your query was ambiguous. Multiple possible variants found:

• chr4-35409009-T-C
• chr4-35409009-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 0.44 in 152,008 control chromosomes in the GnomAD database, including 17,108 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 0.44 (17108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 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: 0.440 AC: 66867 AN: 151890 Hom.: 17111 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.440 AC: 66871 AN: 152008 Hom.: 17108 Cov.: 32 AF XY: 0.443 AC XY: 32941 AN XY: 74286

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.476

Alfa AF: 0.536 Hom.: 34488

Bravo AF: 0.431

Asia WGS AF: 0.523 AC: 1817 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533317; hg19: chr4-35410631;