rs4833826

Variant names:

• chr4-122432762-A-G
• rs4833826

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.248 in 152,090 control chromosomes in the GnomAD database, including 5,689 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 0.25 (5689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 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: 0.248 AC: 37753 AN: 151972 Hom.: 5675 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.248 AC: 37787 AN: 152090 Hom.: 5689 Cov.: 32 AF XY: 0.254 AC XY: 18901 AN XY: 74312

African (AFR) AF: 0.0737 AC: 3060 AN: 41530

American (AMR) AF: 0.300 AC: 4579 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1746 AN: 5162

South Asian (SAS) AF: 0.505 AC: 2431 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3079 AN: 10552

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20297 AN: 67972

Other (OTH) AF: 0.303 AC: 638 AN: 2108

Alfa AF: 0.271 Hom.: 1356

Bravo AF: 0.237

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.5
DANN	Benign	0.69
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs4833826; hg19: chr4-123353917;