ENST00000779509.1:n.138+10906G>A

Variant names:

• chr11-69207088-G-A
• rs12793759
• ENST00000779509.1:n.138+10906G>A

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+10906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,992 control chromosomes in the GnomAD database, including 1,172 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 (1172 hom., cov: 32)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 17 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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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+10906G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17492 AN: 151874 Hom.: 1172 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.115 AC: 17485 AN: 151992 Hom.: 1172 Cov.: 32 AF XY: 0.112 AC XY: 8296 AN XY: 74282

African (AFR) AF: 0.0635 AC: 2632 AN: 41442

American (AMR) AF: 0.106 AC: 1627 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 754 AN: 3466

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5168

South Asian (SAS) AF: 0.0734 AC: 353 AN: 4808

European-Finnish (FIN) AF: 0.0788 AC: 831 AN: 10542

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10740 AN: 67966

Other (OTH) AF: 0.149 AC: 315 AN: 2108

Alfa AF: 0.143 Hom.: 873

Bravo AF: 0.117

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.9
DANN	Benign	0.83
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12793759; hg19: chr11-68974555;