rs288496

Variant names:

• chr3-69582898-A-G
• rs288496

Your query was ambiguous. Multiple possible variants found:

• chr3-69582898-A-G
• chr3-69582898-A-T

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 0.722 in 151,988 control chromosomes in the GnomAD database, including 40,434 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 0.72 (40434 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.722 AC: 109618 AN: 151870 Hom.: 40411 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.722 AC: 109686 AN: 151988 Hom.: 40434 Cov.: 31 AF XY: 0.722 AC XY: 53609 AN XY: 74260

African (AFR) AF: 0.856 AC: 35542 AN: 41500

American (AMR) AF: 0.750 AC: 11424 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2262 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4439 AN: 5162

South Asian (SAS) AF: 0.765 AC: 3681 AN: 4814

European-Finnish (FIN) AF: 0.604 AC: 6352 AN: 10524

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43880 AN: 67962

Other (OTH) AF: 0.680 AC: 1436 AN: 2112

Alfa AF: 0.662 Hom.: 49826

Bravo AF: 0.738

Asia WGS AF: 0.811 AC: 2819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs288496; hg19: chr3-69632049;