rs9506969

Variant names:

• chr13-22922858-G-A
• rs9506969
• ENST00000575845.1:n.87-1246G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-22922858-G-A
• chr13-22922858-G-T

Variant summary

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

The ENST00000575845.1(ENSG00000262198):​n.87-1246G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,090 control chromosomes in the GnomAD database, including 21,697 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 0.50 (21697 hom., cov: 33)
• Consequence: ENSG00000262198 ENST00000575845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

ENSG00000262198 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262198	ENST00000575845.1	n.87-1246G>A		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76289 AN: 151972 Hom.: 21705 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.502 AC: 76284 AN: 152090 Hom.: 21697 Cov.: 33 AF XY: 0.506 AC XY: 37620 AN XY: 74340

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.522

Alfa AF: 0.597 Hom.: 33399

Bravo AF: 0.472

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9506969; hg19: chr13-23496997;