rs166583

Positions:

• chr4-58067170-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;