6-85678391-G-C

Variant summary

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

The ENST00000369605.9(SNHG5):​n.342C>G 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 0.746 in 152,196 control chromosomes in the GnomAD database, including 43,793 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 0.75 ( 43790 hom., cov: 34)
Exomes 𝑓: 0.57 ( 3 hom. )

Consequence

SNHG5
ENST00000369605.9 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08
Variant links:
Genes affected
SNHG5 (HGNC:21026): (small nucleolar RNA host gene 5) This gene represent a snoRNA host gene and produces a long non-coding RNA. This RNA may regulate gene expression by acting as a sponge for microRNAs. This transcript may also stabilize mRNAs by blocking degradation by staufen double-stranded RNA binding protein 1. [provided by RefSeq, Dec 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNHG5NR_003038.2 linkn.41-203C>G intron_variant Intron 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNHG5ENST00000369605.9 linkn.342C>G non_coding_transcript_exon_variant Exon 1 of 5 1
SNHG5ENST00000420199.6 linkn.358C>G non_coding_transcript_exon_variant Exon 1 of 4 3
SNHG5ENST00000428833.6 linkn.358C>G non_coding_transcript_exon_variant Exon 1 of 4 2

Frequencies

GnomAD3 genomes
AF:
0.746
AC:
113405
AN:
152064
Hom.:
43729
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.938
Gnomad AMI
AF:
0.765
Gnomad AMR
AF:
0.807
Gnomad ASJ
AF:
0.734
Gnomad EAS
AF:
0.646
Gnomad SAS
AF:
0.804
Gnomad FIN
AF:
0.610
Gnomad MID
AF:
0.816
Gnomad NFE
AF:
0.640
Gnomad OTH
AF:
0.733
GnomAD4 exome
AF:
0.571
AC:
8
AN:
14
Hom.:
3
Cov.:
0
AF XY:
0.400
AC XY:
4
AN XY:
10
show subpopulations
Gnomad4 AFR exome
AF:
1.00
Gnomad4 FIN exome
AF:
0.250
Gnomad4 NFE exome
AF:
0.500
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.746
AC:
113528
AN:
152182
Hom.:
43790
Cov.:
34
AF XY:
0.747
AC XY:
55585
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.938
Gnomad4 AMR
AF:
0.807
Gnomad4 ASJ
AF:
0.734
Gnomad4 EAS
AF:
0.646
Gnomad4 SAS
AF:
0.804
Gnomad4 FIN
AF:
0.610
Gnomad4 NFE
AF:
0.640
Gnomad4 OTH
AF:
0.734
Alfa
AF:
0.582
Hom.:
1757
Bravo
AF:
0.769
Asia WGS
AF:
0.738
AC:
2566
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
2.3
DANN
Benign
0.45

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.

Other links and lift over

dbSNP: rs1059306; hg19: chr6-86388109; API