rs11582403

Variant names:

• chr1-46748281-C-G
• rs11582403

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.122 in 152,148 control chromosomes in the GnomAD database, including 1,447 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 0.12 (1447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.121 AC: 18459 AN: 152030 Hom.: 1433 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.0358

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.122 AC: 18511 AN: 152148 Hom.: 1447 Cov.: 32 AF XY: 0.123 AC XY: 9133 AN XY: 74380

African (AFR) AF: 0.212 AC: 8785 AN: 41464

American (AMR) AF: 0.0965 AC: 1477 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3470

East Asian (EAS) AF: 0.0357 AC: 185 AN: 5178

South Asian (SAS) AF: 0.183 AC: 884 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10594

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0786 AC: 5342 AN: 68006

Other (OTH) AF: 0.121 AC: 255 AN: 2114

Alfa AF: 0.107 Hom.: 153

Bravo AF: 0.121

Asia WGS AF: 0.0900 AC: 315 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	0.15
DANN	Benign	0.37
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs11582403; hg19: chr1-47213953;