rs4833467

chr4-114746031-A-Gchr4-114746031-A-T

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 0.643 in 151,922 control chromosomes in the GnomAD database, including 32,195 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 0.64 (32195 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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: 0.643 AC: 97592 AN: 151804 Hom.: 32138 Cov.: 30

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.643 AC: 97712 AN: 151922 Hom.: 32195 Cov.: 30 AF XY: 0.648 AC XY: 48139 AN XY: 74242

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.627

Alfa AF: 0.568 Hom.: 33907

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.47
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833467; hg19: chr4-115667187;