Variant 7-22868624-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000656301.1(SNHG26):n.554-3870G>A 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

SNHG26
ENST00000656301.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.446

Variant links:

Genes affected

ENSG00000226329 (HGNC:):

ENSG00000226329 links:

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

SNHG26 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000226329	ENST00000452069.1 link	n.1040-676C>T	intron_variant	6
SNHG26	ENST00000656301.1 link	n.554-3870G>A	intron_variant
SNHG26	ENST00000685098.2 link	n.198-3870G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89415

AN:

151728

Hom.:

27700

Cov.:

show subpopulations

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.:

AF XY:

0.593

AC XY:

44036

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.777

Gnomad4 AMR

AF:

0.613

Gnomad4 ASJ

AF:

0.402

Gnomad4 EAS

AF:

0.646

Gnomad4 SAS

AF:

0.638

Gnomad4 FIN

AF:

0.538

Gnomad4 NFE

AF:

0.481

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.570

Hom.:

3706

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over