rs1828390

Variant names:

• chr11-41900635-T-C
• rs1828390

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.205 in 152,062 control chromosomes in the GnomAD database, including 5,015 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 0.20 (5015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.205 AC: 31080 AN: 151944 Hom.: 5005 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0929

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.205 AC: 31131 AN: 152062 Hom.: 5015 Cov.: 32 AF XY: 0.204 AC XY: 15136 AN XY: 74350

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0929

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.163

Alfa AF: 0.159 Hom.: 412

Bravo AF: 0.217

Asia WGS AF: 0.202 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1828390; hg19: chr11-41922185;