rs3898490

Variant names:

• chr11-130485336-A-G
• rs3898490

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 152,162 control chromosomes in the GnomAD database, including 4,942 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 (4942 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811

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 = 0.355 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: 0.249 AC: 37800 AN: 152044 Hom.: 4928 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.249 AC: 37844 AN: 152162 Hom.: 4942 Cov.: 33 AF XY: 0.249 AC XY: 18527 AN XY: 74388

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.243

Alfa AF: 0.242 Hom.: 566

Bravo AF: 0.240

Asia WGS AF: 0.254 AC: 882 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	4.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3898490; hg19: chr11-130355231;