rs11779265

Variant names:

• chr8-5131619-T-C
• rs11779265
• XR_001745763.2:n.395+13246A>G

Variant summary

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

The XR_001745763.2(LOC107986907):​n.395+13246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,862 control chromosomes in the GnomAD database, including 13,367 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 0.41 (13367 hom., cov: 30)
• Consequence: LOC107986907 XR_001745763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 0 publications found

Genes affected

LOC107986907 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61929 AN: 151744 Hom.: 13344 Cov.: 30

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.408 AC: 61997 AN: 151862 Hom.: 13367 Cov.: 30 AF XY: 0.397 AC XY: 29450 AN XY: 74198

African (AFR) AF: 0.506 AC: 20909 AN: 41358

American (AMR) AF: 0.310 AC: 4736 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1698 AN: 3466

East Asian (EAS) AF: 0.120 AC: 618 AN: 5158

South Asian (SAS) AF: 0.294 AC: 1414 AN: 4806

European-Finnish (FIN) AF: 0.264 AC: 2786 AN: 10544

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28466 AN: 67954

Other (OTH) AF: 0.414 AC: 874 AN: 2110

Alfa AF: 0.416 Hom.: 22844

Bravo AF: 0.415

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs11779265; hg19: chr8-4989141;