rs4833233

chr4-121767589-G-Achr4-121767589-G-Cchr4-121767589-G-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 0.516 in 151,770 control chromosomes in the GnomAD database, including 20,377 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 0.52 (20377 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.552 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: 0.516 AC: 78193 AN: 151652 Hom.: 20361 Cov.: 30

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.516 AC: 78262 AN: 151770 Hom.: 20377 Cov.: 30 AF XY: 0.515 AC XY: 38153 AN XY: 74152

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.511

Alfa AF: 0.503 Hom.: 39726

Bravo AF: 0.524

Asia WGS AF: 0.515 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	13
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833233; hg19: chr4-122688744;