rs11216126

Variant names:

• chr11-116746524-A-C
• rs11216126
• ENST00000836679.1:n.433+8010A>C

Variant summary

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

The ENST00000836679.1(ENSG00000308823):​n.433+8010A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,248 control chromosomes in the GnomAD database, including 1,348 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 (1348 hom., cov: 32)
• Consequence: ENSG00000308823 ENST00000836679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779
• Publications: 51 publications found

Genes affected

ENSG00000308823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 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
ENSG00000308823	ENST00000836679.1	n.433+8010A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17657 AN: 152130 Hom.: 1347 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.116 AC: 17665 AN: 152248 Hom.: 1348 Cov.: 32 AF XY: 0.122 AC XY: 9117 AN XY: 74442

African (AFR) AF: 0.0456 AC: 1897 AN: 41566

American (AMR) AF: 0.139 AC: 2133 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4822

European-Finnish (FIN) AF: 0.174 AC: 1842 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8634 AN: 68008

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.123 Hom.: 4758

Bravo AF: 0.107

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs11216126; hg19: chr11-116617240;