rs11036238

Variant names:

• chr11-5204405-G-C
• rs11036238

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 0.213 in 152,120 control chromosomes in the GnomAD database, including 3,975 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 0.21 (3975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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: 0.214 AC: 32470 AN: 152004 Hom.: 3972 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.213 AC: 32474 AN: 152120 Hom.: 3975 Cov.: 32 AF XY: 0.212 AC XY: 15762 AN XY: 74360

African (AFR) AF: 0.114 AC: 4735 AN: 41522

American (AMR) AF: 0.212 AC: 3241 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3470

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5176

South Asian (SAS) AF: 0.200 AC: 963 AN: 4826

European-Finnish (FIN) AF: 0.254 AC: 2677 AN: 10554

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18883 AN: 67968

Other (OTH) AF: 0.250 AC: 528 AN: 2114

Alfa AF: 0.261 Hom.: 3133

Bravo AF: 0.203

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs11036238; hg19: chr11-5225635;