3-87283562-G-T

Variant names:

• chr3-87283562-G-T
• rs300996

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 0.391 in 151,614 control chromosomes in the GnomAD database, including 12,024 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 0.39 (12024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.547 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: 0.391 AC: 59249 AN: 151494 Hom.: 12016 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.391 AC: 59296 AN: 151614 Hom.: 12024 Cov.: 32 AF XY: 0.398 AC XY: 29500 AN XY: 74046

African (AFR) AF: 0.290 AC: 11994 AN: 41394

American (AMR) AF: 0.457 AC: 6963 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1384 AN: 3464

East Asian (EAS) AF: 0.503 AC: 2584 AN: 5136

South Asian (SAS) AF: 0.564 AC: 2713 AN: 4808

European-Finnish (FIN) AF: 0.434 AC: 4547 AN: 10486

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27855 AN: 67782

Other (OTH) AF: 0.401 AC: 844 AN: 2106

Alfa AF: 0.401 Hom.: 5372

Bravo AF: 0.385

Asia WGS AF: 0.511 AC: 1770 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.40
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs300996; hg19: chr3-87332712;