3-88483065-G-A

Variant names:

• chr3-88483065-G-A
• rs2344953

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 0.262 in 151,638 control chromosomes in the GnomAD database, including 5,834 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 0.26 (5834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39657 AN: 151520 Hom.: 5816 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.262 AC: 39705 AN: 151638 Hom.: 5834 Cov.: 32 AF XY: 0.270 AC XY: 20027 AN XY: 74048

African (AFR) AF: 0.148 AC: 6122 AN: 41444

American (AMR) AF: 0.426 AC: 6459 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3464

East Asian (EAS) AF: 0.310 AC: 1595 AN: 5140

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4818

European-Finnish (FIN) AF: 0.377 AC: 3971 AN: 10536

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18049 AN: 67770

Other (OTH) AF: 0.279 AC: 587 AN: 2104

Alfa AF: 0.266 Hom.: 2965

Bravo AF: 0.266

Asia WGS AF: 0.308 AC: 1067 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs2344953; hg19: chr3-88532215;