rs10809546

chr9-11652121-A-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, non coding transcript 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: ENST00000649122.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649122.1	n.204+11287A>T		intron_variant, non_coding_transcript_variant

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;