4-186063586-A-G

Variant names:

• chr4-186063586-A-G
• rs4861699

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 0.846 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.876 AC: 36387 AN: 41530

American (AMR) AF: 0.875 AC: 13386 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3077 AN: 3466

East Asian (EAS) AF: 0.755 AC: 3907 AN: 5172

South Asian (SAS) AF: 0.837 AC: 4041 AN: 4826

European-Finnish (FIN) AF: 0.755 AC: 7984 AN: 10570

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56947 AN: 68012

Other (OTH) AF: 0.879 AC: 1857 AN: 2112

Alfa AF: 0.822 Hom.: 11981

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4861699; hg19: chr4-186984740;