4-20086436-G-C

Variant names:

• chr4-20086436-G-C
• rs1905843

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 0.801 in 152,052 control chromosomes in the GnomAD database, including 49,591 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 0.80 (49591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.854 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: 0.801 AC: 121685 AN: 151936 Hom.: 49574 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.801 AC: 121753 AN: 152052 Hom.: 49591 Cov.: 32 AF XY: 0.804 AC XY: 59793 AN XY: 74334

African (AFR) AF: 0.639 AC: 26449 AN: 41394

American (AMR) AF: 0.859 AC: 13119 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3144 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4084 AN: 5154

South Asian (SAS) AF: 0.855 AC: 4120 AN: 4818

European-Finnish (FIN) AF: 0.908 AC: 9630 AN: 10600

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58464 AN: 68016

Other (OTH) AF: 0.816 AC: 1727 AN: 2116

Alfa AF: 0.826 Hom.: 6574

Bravo AF: 0.791

Asia WGS AF: 0.773 AC: 2687 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1905843; hg19: chr4-20088059;