rs1828390

Variant names:

• chr11-41900635-T-C
• rs1828390

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.447 AC: 18512 AN: 41430

American (AMR) AF: 0.117 AC: 1794 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3468

East Asian (EAS) AF: 0.222 AC: 1143 AN: 5154

South Asian (SAS) AF: 0.184 AC: 889 AN: 4824

European-Finnish (FIN) AF: 0.0929 AC: 986 AN: 10608

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7034 AN: 67988

Other (OTH) AF: 0.163 AC: 343 AN: 2108

Alfa AF: 0.170 Hom.: 491

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
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1828390; hg19: chr11-41922185;