11-69209529-A-G

Variant names:

• chr11-69209529-A-G
• rs11228563
• ENST00000779509.1:n.138+13347A>G

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+13347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,992 control chromosomes in the GnomAD database, including 5,594 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 0.26 (5594 hom., cov: 32)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 3 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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
ENSG00000301530	ENST00000779509.1	n.138+13347A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39797 AN: 151874 Hom.: 5587 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.262 AC: 39831 AN: 151992 Hom.: 5594 Cov.: 32 AF XY: 0.259 AC XY: 19272 AN XY: 74284

African (AFR) AF: 0.246 AC: 10215 AN: 41456

American (AMR) AF: 0.217 AC: 3312 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3470

East Asian (EAS) AF: 0.0138 AC: 71 AN: 5156

South Asian (SAS) AF: 0.130 AC: 624 AN: 4814

European-Finnish (FIN) AF: 0.319 AC: 3367 AN: 10554

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 19959 AN: 67946

Other (OTH) AF: 0.281 AC: 593 AN: 2110

Alfa AF: 0.282 Hom.: 22699

Bravo AF: 0.258

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.031
DANN	Benign	0.11
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs11228563; hg19: chr11-68976996;