6-85678391-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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	ENST00000420199.7	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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.746 AC: 113528 AN: 152182 Hom.: 43790 Cov.: 34 AF XY: 0.747 AC XY: 55585 AN XY: 74388

African (AFR) AF: 0.938 AC: 38978 AN: 41558

American (AMR) AF: 0.807 AC: 12341 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2549 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3330 AN: 5152

South Asian (SAS) AF: 0.804 AC: 3881 AN: 4828

European-Finnish (FIN) AF: 0.610 AC: 6456 AN: 10580

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43509 AN: 67982

Other (OTH) AF: 0.734 AC: 1550 AN: 2112

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1059306; hg19: chr6-86388109;