Variant 11-62855819-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The ENST00000537925.5(SNHG1):n.48dupT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00829 in 357,422 control chromosomes in the GnomAD database, including 44 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0054 ( 12 hom., cov: 33)

Exomes 𝑓: 0.010 ( 32 hom. )

Consequence

SNHG1
ENST00000537925.5 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Variant links:

Genes affected

SNHG1 (HGNC:):

SNHG1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0054 (822/152326) while in subpopulation SAS AF= 0.0309 (149/4828). AF 95% confidence interval is 0.0268. There are 12 homozygotes in gnomad4. There are 413 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
SNHG1	NR_152575.1 linkuse as main transcript	n.66dupT	non_coding_transcript_exon_variant	1/10
SNHG1	NR_152576.1 linkuse as main transcript	n.66dupT	non_coding_transcript_exon_variant	1/10
SNHG1	NR_152584.1 linkuse as main transcript	n.66dupT	non_coding_transcript_exon_variant	1/11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
SNHG1	ENST00000537925.5 linkuse as main transcript	n.48dupT	non_coding_transcript_exon_variant	1/10	1
SNHG1	ENST00000540725.6 linkuse as main transcript	n.21+45dupT	intron_variant		1
SNHG1	ENST00000535076.6 linkuse as main transcript	n.4dupT	non_coding_transcript_exon_variant	1/5	2

Frequencies

GnomAD3 genomes

AF:

0.00541

AC:

823

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.00380

Gnomad ASJ

AF:

0.00547

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0308

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00686

Gnomad OTH

AF:

0.00860

GnomAD4 exome

AF:

0.0104

AC:

2142

AN:

205096

Hom.:

Cov.:

AF XY:

0.0126

AC XY:

1428

AN XY:

113476

show subpopulations

Gnomad4 AFR exome

AF:

0.00112

Gnomad4 AMR exome

AF:

0.00379

Gnomad4 ASJ exome

AF:

0.00238

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0257

Gnomad4 FIN exome

AF:

0.00619

Gnomad4 NFE exome

AF:

0.00730

Gnomad4 OTH exome

AF:

0.00949

GnomAD4 genome

AF:

0.00540

AC:

822

AN:

152326

Hom.:

Cov.:

AF XY:

0.00554

AC XY:

413

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00379

Gnomad4 ASJ

AF:

0.00547

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0309

Gnomad4 FIN

AF:

0.00443

Gnomad4 NFE

AF:

0.00686

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.00698

Hom.:

Bravo

AF:

0.00469

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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