rs4833248

chr4-122459250-G-Achr4-122459250-G-C

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 0.249 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.248 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

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.302

Alfa AF: 0.228 Hom.: 1368

Bravo AF: 0.237

Asia WGS AF: 0.422 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.7
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833248; hg19: chr4-123380405;