ENST00000720573.1:n.748+8539T>C

Variant names:

• chr9-1202371-A-G
• rs10809650
• ENST00000720573.1:n.748+8539T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000720573.1(ENSG00000294012):​n.748+8539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,448 control chromosomes in the GnomAD database, including 6,311 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 0.27 (6311 hom., cov: 30)
• Consequence: ENSG00000294012 ENST00000720573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 11 publications found

Genes affected

ENSG00000294012 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 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
ENSG00000294012	ENST00000720573.1	n.748+8539T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40240 AN: 151330 Hom.: 6297 Cov.: 30

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.266 AC: 40296 AN: 151448 Hom.: 6311 Cov.: 30 AF XY: 0.275 AC XY: 20338 AN XY: 73952

African (AFR) AF: 0.137 AC: 5676 AN: 41358

American (AMR) AF: 0.405 AC: 6130 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3466

East Asian (EAS) AF: 0.540 AC: 2756 AN: 5108

South Asian (SAS) AF: 0.244 AC: 1154 AN: 4728

European-Finnish (FIN) AF: 0.400 AC: 4186 AN: 10456

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18845 AN: 67910

Other (OTH) AF: 0.282 AC: 590 AN: 2092

Alfa AF: 0.271 Hom.: 23095

Bravo AF: 0.265

Asia WGS AF: 0.376 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.87
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10809650; hg19: chr9-1202371;