rs4862379

Variant names:

• chr4-184553404-G-A
• rs4862379

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 0.0732 in 152,186 control chromosomes in the GnomAD database, including 453 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 0.073 (453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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 (SAS) allele frequency at 95% confidence interval = 0.077 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: 0.0733 AC: 11144 AN: 152068 Hom.: 452 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.0732 AC: 11147 AN: 152186 Hom.: 453 Cov.: 32 AF XY: 0.0734 AC XY: 5465 AN XY: 74420

Gnomad4 AFR AF: 0.0743

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.0317

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.0826 Hom.: 455

Bravo AF: 0.0765

Asia WGS AF: 0.0470 AC: 163 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	5.1
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4862379; hg19: chr4-185474558;