ENST00000726940.1:n.76+2263T>C

Variant names:

• chr9-120382296-A-G
• rs10818453
• ENST00000726940.1:n.76+2263T>C

Variant summary

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

The ENST00000726940.1(ENSG00000294948):​n.76+2263T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 150,788 control chromosomes in the GnomAD database, including 35,035 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 0.68 (35035 hom., cov: 29)
• Consequence: ENSG00000294948 ENST00000726940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 4 publications found

Genes affected

ENSG00000294948 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726940.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294948	ENST00000726940.1		n.76+2263T>C		intron	N/A
	ENSG00000294948	ENST00000726941.1		n.67-1155T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.681 AC: 102632 AN: 150672 Hom.: 35020 Cov.: 29

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.681 AC: 102691 AN: 150788 Hom.: 35035 Cov.: 29 AF XY: 0.684 AC XY: 50428 AN XY: 73682

African (AFR) AF: 0.633 AC: 25605 AN: 40478

American (AMR) AF: 0.732 AC: 11154 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2285 AN: 3464

East Asian (EAS) AF: 0.765 AC: 3910 AN: 5110

South Asian (SAS) AF: 0.664 AC: 3183 AN: 4792

European-Finnish (FIN) AF: 0.772 AC: 8129 AN: 10526

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46301 AN: 67886

Other (OTH) AF: 0.678 AC: 1423 AN: 2098

Alfa AF: 0.687 Hom.: 15587

Bravo AF: 0.675

Asia WGS AF: 0.719 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10818453; hg19: chr9-123144574;