rs166583

Variant names:

• chr4-58067170-A-G
• rs166583

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 0.301 in 151,760 control chromosomes in the GnomAD database, including 7,056 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 0.30 (7056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 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: 0.301 AC: 45679 AN: 151642 Hom.: 7057 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.301 AC: 45689 AN: 151760 Hom.: 7056 Cov.: 32 AF XY: 0.299 AC XY: 22140 AN XY: 74154

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.319

Alfa AF: 0.319 Hom.: 3521

Bravo AF: 0.299

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166583; hg19: chr4-58933336;