rs4862379

Positions:

• chr4-184553404-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;