chr13-86858787-A-G

Variant names:

• chr13-86858787-A-G
• rs9523562
• XR_931621.3:n.362-24168A>G

Variant summary

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

The XR_931621.3(LOC105370300):​n.362-24168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,842 control chromosomes in the GnomAD database, including 18,595 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 (18595 hom., cov: 32)
• Consequence: LOC105370300 XR_931621.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 1 publications found

Genes affected

LOC105370300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74398 AN: 151724 Hom.: 18549 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.491 AC: 74504 AN: 151842 Hom.: 18595 Cov.: 32 AF XY: 0.492 AC XY: 36516 AN XY: 74188

African (AFR) AF: 0.550 AC: 22778 AN: 41398

American (AMR) AF: 0.522 AC: 7964 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3426 AN: 5144

South Asian (SAS) AF: 0.584 AC: 2816 AN: 4820

European-Finnish (FIN) AF: 0.433 AC: 4557 AN: 10520

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30094 AN: 67906

Other (OTH) AF: 0.481 AC: 1017 AN: 2114

Alfa AF: 0.471 Hom.: 2831

Bravo AF: 0.501

Asia WGS AF: 0.613 AC: 2133 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.55
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs9523562; hg19: chr13-87511042; COSMIC: COSV64441743;