chr3-5420855-G-A

Variant names:

• chr3-5420855-G-A
• rs4684484

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 0.389 in 152,078 control chromosomes in the GnomAD database, including 13,169 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 (13169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 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: 0.390 AC: 59236 AN: 151960 Hom.: 13173 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.389 AC: 59231 AN: 152078 Hom.: 13169 Cov.: 32 AF XY: 0.391 AC XY: 29075 AN XY: 74310

African (AFR) AF: 0.177 AC: 7332 AN: 41506

American (AMR) AF: 0.390 AC: 5955 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1754 AN: 5154

South Asian (SAS) AF: 0.268 AC: 1287 AN: 4810

European-Finnish (FIN) AF: 0.573 AC: 6052 AN: 10562

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33692 AN: 67986

Other (OTH) AF: 0.417 AC: 881 AN: 2112

Alfa AF: 0.433 Hom.: 22833

Bravo AF: 0.373

Asia WGS AF: 0.280 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.80
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs4684484; hg19: chr3-5462541;