ENST00000452069.1:n.1040-676C>T

Variant names:

• chr7-22868624-G-A
• rs1581498
• ENST00000452069.1:n.1040-676C>T

Variant summary

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

The ENST00000452069.1(ENSG00000226329):​n.1040-676C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,846 control chromosomes in the GnomAD database, including 27,744 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 0.59 (27744 hom., cov: 31)
• Consequence: ENSG00000226329 ENST00000452069.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 7 publications found

Genes affected

ENSG00000226329 (HGNC:):

SNHG26 (HGNC:53131): (small nucleolar RNA host gene 26)

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 (AFR) allele frequency at 95% confidence interval = 0.77 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
ENSG00000226329	ENST00000452069.1	n.1040-676C>T		intron_variant	Intron 7 of 9	6
SNHG26	ENST00000656301.2	n.554-3870G>A		intron_variant	Intron 5 of 5
SNHG26	ENST00000685098.3	n.199-3870G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89415 AN: 151728 Hom.: 27700 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.589 AC: 89513 AN: 151846 Hom.: 27744 Cov.: 31 AF XY: 0.593 AC XY: 44036 AN XY: 74238

African (AFR) AF: 0.777 AC: 32189 AN: 41404

American (AMR) AF: 0.613 AC: 9359 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1391 AN: 3462

East Asian (EAS) AF: 0.646 AC: 3330 AN: 5154

South Asian (SAS) AF: 0.638 AC: 3063 AN: 4804

European-Finnish (FIN) AF: 0.538 AC: 5671 AN: 10544

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32666 AN: 67894

Other (OTH) AF: 0.542 AC: 1143 AN: 2108

Alfa AF: 0.625 Hom.: 12439

Bravo AF: 0.603

Asia WGS AF: 0.633 AC: 2202 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	0.27
DANN	Benign	0.52
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1581498; hg19: chr7-22908243;