rs11229030

Variant names:

• chr11-57435536-C-T
• rs11229030

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 0.558 in 152,070 control chromosomes in the GnomAD database, including 25,016 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 0.56 (25016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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: 0.558 AC: 84749 AN: 151952 Hom.: 25006 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.558 AC: 84786 AN: 152070 Hom.: 25016 Cov.: 32 AF XY: 0.566 AC XY: 42097 AN XY: 74348

African (AFR) AF: 0.357 AC: 14799 AN: 41468

American (AMR) AF: 0.684 AC: 10452 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2420 AN: 3470

East Asian (EAS) AF: 0.834 AC: 4315 AN: 5174

South Asian (SAS) AF: 0.681 AC: 3284 AN: 4824

European-Finnish (FIN) AF: 0.604 AC: 6391 AN: 10578

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41034 AN: 67964

Other (OTH) AF: 0.588 AC: 1241 AN: 2112

Alfa AF: 0.598 Hom.: 128900

Bravo AF: 0.557

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.87
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11229030; hg19: chr11-57203009;