3-5290580-G-T

Variant names:

• chr3-5290580-G-T
• rs9311480

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 0.524 in 152,082 control chromosomes in the GnomAD database, including 23,518 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 0.52 (23518 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

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 = 0.671 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: 0.524 AC: 79650 AN: 151964 Hom.: 23508 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.524 AC: 79692 AN: 152082 Hom.: 23518 Cov.: 33 AF XY: 0.531 AC XY: 39448 AN XY: 74348

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.539

Alfa AF: 0.616 Hom.: 45843

Bravo AF: 0.501

Asia WGS AF: 0.559 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9311480; hg19: chr3-5332265;