rs4861722

Variant names:

• chr4-186568229-G-A
• rs4861722

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 0.569 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

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 = 0.661 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: 0.569 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

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.598

Alfa AF: 0.626 Hom.: 14244

Bravo AF: 0.556

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4861722; hg19: chr4-187489383;