rs10809546

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649122.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000285784	ENST00000649122.1		n.204+11287A>T		intron	N/A

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

African (AFR) AF: 0.197 AC: 8163 AN: 41416

American (AMR) AF: 0.198 AC: 2995 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1197 AN: 5140

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4822

European-Finnish (FIN) AF: 0.191 AC: 2018 AN: 10568

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13515 AN: 67862

Other (OTH) AF: 0.211 AC: 445 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.46
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10809546; hg19: chr9-11652121;