4-20086436-G-C

Position:

• chr4-20086436-G-C

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 0.801 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.816

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1905843; hg19: chr4-20088059;