ENST00000732866.1:n.118+25436C>T

Variant names:

• chr9-25452814-G-A
• rs13300284
• ENST00000732866.1:n.118+25436C>T

Variant summary

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

The ENST00000732866.1(ENSG00000295812):​n.118+25436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,132 control chromosomes in the GnomAD database, including 195 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 0.041 (195 hom., cov: 31)
• Consequence: ENSG00000295812 ENST00000732866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 11 publications found

Genes affected

ENSG00000295812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.071 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
ENSG00000295812	ENST00000732866.1	n.118+25436C>T		intron_variant	Intron 1 of 4
ENSG00000295812	ENST00000732867.1	n.107+9786C>T		intron_variant	Intron 1 of 4
ENSG00000295812	ENST00000732868.1	n.95+9786C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6182 AN: 152014 Hom.: 195 Cov.: 31

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0312

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

GnomAD4 genome AF: 0.0406 AC: 6180 AN: 152132 Hom.: 195 Cov.: 31 AF XY: 0.0400 AC XY: 2979 AN XY: 74388

African (AFR) AF: 0.0115 AC: 479 AN: 41514

American (AMR) AF: 0.0746 AC: 1139 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3468

East Asian (EAS) AF: 0.0172 AC: 89 AN: 5178

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4820

European-Finnish (FIN) AF: 0.0438 AC: 464 AN: 10584

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0543 AC: 3693 AN: 67996

Other (OTH) AF: 0.0309 AC: 65 AN: 2104

Alfa AF: 0.0493 Hom.: 811

Bravo AF: 0.0431

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs13300284; hg19: chr9-25452812;