rs4684484

Positions:

• chr3-5420855-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.417

Alfa AF: 0.470 Hom.: 16096

Bravo AF: 0.373

Asia WGS AF: 0.280 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4684484; hg19: chr3-5462541;