ENST00000779509.1:n.139-6714G>T

Variant names:

• chr11-69241647-G-T
• rs11228583
• ENST00000779509.1:n.139-6714G>T

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-6714G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,218 control chromosomes in the GnomAD database, including 19,622 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 0.49 (19622 hom., cov: 34)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 16 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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.139-6714G>T		intron_variant	Intron 1 of 3
ENSG00000301530	ENST00000779510.1	n.76+6511G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75167 AN: 152100 Hom.: 19584 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.494 AC: 75256 AN: 152218 Hom.: 19622 Cov.: 34 AF XY: 0.488 AC XY: 36303 AN XY: 74436

African (AFR) AF: 0.584 AC: 24268 AN: 41536

American (AMR) AF: 0.385 AC: 5893 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3468

East Asian (EAS) AF: 0.0547 AC: 284 AN: 5188

South Asian (SAS) AF: 0.322 AC: 1558 AN: 4834

European-Finnish (FIN) AF: 0.469 AC: 4965 AN: 10582

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34342 AN: 67998

Other (OTH) AF: 0.518 AC: 1093 AN: 2112

Alfa AF: 0.498 Hom.: 2375

Bravo AF: 0.494

Asia WGS AF: 0.282 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.78
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs11228583; hg19: chr11-69009114;