11-133542596-C-A

Variant names:

• chr11-133542596-C-A
• rs11223500
• ENST00000663344.1:n.295-6686C>A

Variant summary

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

The ENST00000663344.1(ENSG00000287068):​n.295-6686C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,070 control chromosomes in the GnomAD database, including 4,989 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 0.23 (4989 hom., cov: 33)
• Consequence: ENSG00000287068 ENST00000663344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 2 publications found

Genes affected

ENSG00000287068 (HGNC:):

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 = 0.39 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
ENSG00000287068	ENST00000663344.1	n.295-6686C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34788 AN: 151952 Hom.: 4974 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.229 AC: 34847 AN: 152070 Hom.: 4989 Cov.: 33 AF XY: 0.235 AC XY: 17451 AN XY: 74328

African (AFR) AF: 0.396 AC: 16399 AN: 41462

American (AMR) AF: 0.205 AC: 3129 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1639 AN: 5160

South Asian (SAS) AF: 0.308 AC: 1483 AN: 4816

European-Finnish (FIN) AF: 0.206 AC: 2181 AN: 10568

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8859 AN: 68006

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.150 Hom.: 3681

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.41
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs11223500; hg19: chr11-133412491;