rs4861722

Variant names:

• chr4-186568229-G-A
• rs4861722

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 0.569 in 152,082 control chromosomes in the GnomAD database, including 25,862 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 0.57 (25862 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 4 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 = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86453 AN: 151962 Hom.: 25850 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.569 AC: 86497 AN: 152082 Hom.: 25862 Cov.: 33 AF XY: 0.564 AC XY: 41950 AN XY: 74346

African (AFR) AF: 0.425 AC: 17595 AN: 41448

American (AMR) AF: 0.578 AC: 8833 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2356 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5174

South Asian (SAS) AF: 0.451 AC: 2176 AN: 4822

European-Finnish (FIN) AF: 0.647 AC: 6834 AN: 10566

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45302 AN: 67996

Other (OTH) AF: 0.598 AC: 1263 AN: 2112

Alfa AF: 0.612 Hom.: 20757

Bravo AF: 0.556

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.42
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs4861722; hg19: chr4-187489383;