rs9523562

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370300	XR_931621.3	n.362-24168A>G		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.490 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 v4.3

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;