chr3-5290580-G-T

Variant names:

• chr3-5290580-G-T
• rs9311480

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 0.524 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.237 AC: 9824 AN: 41466

American (AMR) AF: 0.582 AC: 8894 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2102 AN: 3470

East Asian (EAS) AF: 0.690 AC: 3565 AN: 5168

South Asian (SAS) AF: 0.494 AC: 2380 AN: 4816

European-Finnish (FIN) AF: 0.744 AC: 7870 AN: 10578

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43284 AN: 67982

Other (OTH) AF: 0.539 AC: 1140 AN: 2114

Alfa AF: 0.600 Hom.: 104742

Bravo AF: 0.501

Asia WGS AF: 0.559 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.40
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs9311480; hg19: chr3-5332265;