rs11779265

chr8-5131619-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745763.2(LOC107986907):n.395+13246A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

Genes affected

LOC107986907 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107986907	XR_001745763.2	n.395+13246A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.414

Alfa AF: 0.415 Hom.: 18014

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11779265; hg19: chr8-4989141;