6-85678391-G-C

Variant names:

• chr6-85678391-G-C
• rs1059306
• ENST00000369605.9:n.342C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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]

ENSG00000271793 (HGNC:):

ACMG classification

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
SNHG5	NR_003038.2	n.41-203C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG5	ENST00000369605.9	n.342C>G		non_coding_transcript_exon_variant	Exon 1 of 5	1
SNHG5	ENST00000420199.6	n.358C>G		non_coding_transcript_exon_variant	Exon 1 of 4	3
SNHG5	ENST00000428833.6	n.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

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

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

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

Other links and lift over

dbSNP: rs1059306; hg19: chr6-86388109;