rs11603258

Variant names:

• chr11-80683518-A-G
• rs11603258

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 0.533 in 151,888 control chromosomes in the GnomAD database, including 24,887 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 0.53 (24887 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 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: 0.533 AC: 80893 AN: 151770 Hom.: 24873 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.533 AC: 80927 AN: 151888 Hom.: 24887 Cov.: 31 AF XY: 0.538 AC XY: 39908 AN XY: 74224

African (AFR) AF: 0.214 AC: 8863 AN: 41422

American (AMR) AF: 0.675 AC: 10280 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1739 AN: 5140

South Asian (SAS) AF: 0.723 AC: 3487 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6917 AN: 10546

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45669 AN: 67932

Other (OTH) AF: 0.534 AC: 1124 AN: 2106

Alfa AF: 0.642 Hom.: 50211

Bravo AF: 0.516

Asia WGS AF: 0.537 AC: 1865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.87
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs11603258; hg19: chr11-80394562;