4-120592060-A-G

Variant names:

• chr4-120592060-A-G
• rs10017284

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 0.46 in 151,858 control chromosomes in the GnomAD database, including 16,194 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 0.46 (16194 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 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: 0.460 AC: 69849 AN: 151740 Hom.: 16188 Cov.: 30

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.460 AC: 69888 AN: 151858 Hom.: 16194 Cov.: 30 AF XY: 0.461 AC XY: 34252 AN XY: 74224

African (AFR) AF: 0.422 AC: 17476 AN: 41404

American (AMR) AF: 0.452 AC: 6889 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1670 AN: 3472

East Asian (EAS) AF: 0.417 AC: 2131 AN: 5116

South Asian (SAS) AF: 0.513 AC: 2470 AN: 4812

European-Finnish (FIN) AF: 0.514 AC: 5429 AN: 10564

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32189 AN: 67926

Other (OTH) AF: 0.445 AC: 938 AN: 2108

Alfa AF: 0.462 Hom.: 38869

Bravo AF: 0.451

Asia WGS AF: 0.509 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.1
DANN	Benign	0.90
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10017284; hg19: chr4-121513215;