ENST00000722823.1:n.495+9081C>T

Variant names:

• chr11-39171739-C-T
• rs17712923
• ENST00000722823.1:n.495+9081C>T

Variant summary

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

The ENST00000722823.1(ENSG00000294334):​n.495+9081C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,912 control chromosomes in the GnomAD database, including 3,846 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 (3846 hom., cov: 31)
• Consequence: ENSG00000294334 ENST00000722823.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 0 publications found

Genes affected

ENSG00000294334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722823.1. 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
	ENSG00000294334	ENST00000722823.1		n.495+9081C>T		intron	N/A
	ENSG00000294334	ENST00000722824.1		n.207+9081C>T		intron	N/A
	ENSG00000294334	ENST00000722825.1		n.248+9081C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31097 AN: 151794 Hom.: 3847 Cov.: 31

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0355

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.205 AC: 31089 AN: 151912 Hom.: 3846 Cov.: 31 AF XY: 0.203 AC XY: 15046 AN XY: 74250

African (AFR) AF: 0.0938 AC: 3891 AN: 41466

American (AMR) AF: 0.160 AC: 2435 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3468

East Asian (EAS) AF: 0.0356 AC: 183 AN: 5140

South Asian (SAS) AF: 0.119 AC: 571 AN: 4794

European-Finnish (FIN) AF: 0.339 AC: 3576 AN: 10564

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18866 AN: 67920

Other (OTH) AF: 0.197 AC: 415 AN: 2106

Alfa AF: 0.239 Hom.: 845

Bravo AF: 0.188

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.73
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17712923; hg19: chr11-39193289;