rs4833248

Variant names:

• chr4-122459250-G-A
• rs4833248

Your query was ambiguous. Multiple possible variants found:

• chr4-122459250-G-A
• chr4-122459250-G-C

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 0.249 in 151,814 control chromosomes in the GnomAD database, including 5,685 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 (5685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37694 AN: 151694 Hom.: 5671 Cov.: 31

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.249 AC: 37728 AN: 151814 Hom.: 5685 Cov.: 31 AF XY: 0.255 AC XY: 18899 AN XY: 74210

African (AFR) AF: 0.0737 AC: 3055 AN: 41458

American (AMR) AF: 0.299 AC: 4560 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3464

East Asian (EAS) AF: 0.340 AC: 1744 AN: 5134

South Asian (SAS) AF: 0.505 AC: 2422 AN: 4796

European-Finnish (FIN) AF: 0.294 AC: 3096 AN: 10534

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

European-Non Finnish (NFE) AF: 0.298 AC: 20257 AN: 67880

Other (OTH) AF: 0.302 AC: 638 AN: 2110

Alfa AF: 0.237 Hom.: 1835

Bravo AF: 0.237

Asia WGS AF: 0.422 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.43
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4833248; hg19: chr4-123380405;