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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986907	XR_001745763.2	n.395+13246A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;