rs454530

Variant names:

• chr3-148682870-A-G
• rs454530

Your query was ambiguous. Multiple possible variants found:

• chr3-148682870-A-G
• chr3-148682870-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 0.201 in 152,118 control chromosomes in the GnomAD database, including 3,404 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 0.20 (3404 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30558 AN: 152000 Hom.: 3395 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.201 AC: 30592 AN: 152118 Hom.: 3404 Cov.: 32 AF XY: 0.198 AC XY: 14732 AN XY: 74350

African (AFR) AF: 0.276 AC: 11454 AN: 41498

American (AMR) AF: 0.153 AC: 2329 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3466

East Asian (EAS) AF: 0.118 AC: 609 AN: 5178

South Asian (SAS) AF: 0.126 AC: 607 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1506 AN: 10576

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12337 AN: 67996

Other (OTH) AF: 0.208 AC: 440 AN: 2112

Alfa AF: 0.181 Hom.: 478

Bravo AF: 0.205

Asia WGS AF: 0.131 AC: 462 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	0.47
DANN	Benign	0.72
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs454530; hg19: chr3-148400657;