4-186063586-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 0.846 in 152,184 control chromosomes in the GnomAD database, including 54,573 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 0.85 (54573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.846 AC: 128589 AN: 152066 Hom.: 54515 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.846 AC: 128709 AN: 152184 Hom.: 54573 Cov.: 32 AF XY: 0.841 AC XY: 62553 AN XY: 74402

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.879

Alfa AF: 0.836 Hom.: 6231

Bravo AF: 0.855

Asia WGS AF: 0.805 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4861699; hg19: chr4-186984740;