rs4882017

Variant names:

• chr11-48548630-A-G
• rs4882017

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 0.537 in 152,016 control chromosomes in the GnomAD database, including 23,341 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 0.54 (23341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.537 AC: 81507 AN: 151898 Hom.: 23319 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.537 AC: 81576 AN: 152016 Hom.: 23341 Cov.: 32 AF XY: 0.536 AC XY: 39851 AN XY: 74302

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.559

Alfa AF: 0.597 Hom.: 5884

Bravo AF: 0.529

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4882017; hg19: chr11-48570182;