4-58067170-A-G

Variant names:

• chr4-58067170-A-G
• rs166583

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 0.301 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.277 AC: 11471 AN: 41382

American (AMR) AF: 0.285 AC: 4332 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1524 AN: 3466

East Asian (EAS) AF: 0.126 AC: 644 AN: 5100

South Asian (SAS) AF: 0.342 AC: 1652 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2905 AN: 10568

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22046 AN: 67904

Other (OTH) AF: 0.319 AC: 672 AN: 2108

Alfa AF: 0.320 Hom.: 3990

Bravo AF: 0.299

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.8
DANN	Benign	0.82
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs166583; hg19: chr4-58933336;