rs10809546

Variant names:

• chr9-11652121-A-T
• rs10809546
• ENST00000649122.1:n.204+11287A>T

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.204+11287A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,756 control chromosomes in the GnomAD database, including 3,152 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 0.20 (3152 hom., cov: 31)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 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
ENSG00000285784	ENST00000649122.1	n.204+11287A>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30430 AN: 151638 Hom.: 3147 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.201 AC: 30452 AN: 151756 Hom.: 3152 Cov.: 31 AF XY: 0.203 AC XY: 15014 AN XY: 74104

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.211

Alfa AF: 0.195 Hom.: 368

Bravo AF: 0.201

Asia WGS AF: 0.192 AC: 667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10809546; hg19: chr9-11652121;