rs2304927

Positions:

• chr17-77088760-G-A

Variant summary

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

The NR_027058.1(SNHG20):​n.118G>A 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 0.0378 in 149,106 control chromosomes in the GnomAD database, including 192 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 0.038 (192 hom., cov: 32)
  • Exomes 𝑓: 0.045 (0 hom.)
• Consequence: SNHG20 NR_027058.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

Genes affected

SNHG20 (HGNC:33099): (small nucleolar RNA host gene 20)

SEC14L1 (HGNC:10698): (SEC14 like lipid binding 1) The protein encoded by this gene belongs to the SEC14 cytosolic factor family. It has similarity to yeast SEC14 and to Japanese flying squid RALBP which suggests a possible role of the gene product in an intracellular transport system. Multiple alternatively spliced transcript variants have been found for this gene; some variants represent read-through transcripts that include exons from the upstream gene C17orf86. [provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNHG20	NR_027058.1	n.118G>A		non_coding_transcript_exon_variant	1/3
SEC14L1	NM_001204408.2	c.-548G>A		5_prime_UTR_variant	1/20
SEC14L1	NM_001204410.2	c.-548G>A		5_prime_UTR_variant	1/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG20	ENST00000564414.5	n.149-393G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5629 AN: 148874 Hom.: 194 Cov.: 32

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.0673

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0601

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0417

Gnomad OTH AF: 0.0397

GnomAD4 exome AF: 0.0446 AC: 5 AN: 112 Hom.: 0 Cov.: 0 AF XY: 0.0581 AC XY: 5 AN XY: 86

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0222

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.0378 AC: 5629 AN: 148994 Hom.: 192 Cov.: 32 AF XY: 0.0381 AC XY: 2771 AN XY: 72732

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0219

Gnomad4 ASJ AF: 0.0601

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0463

Gnomad4 NFE AF: 0.0417

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0394 Hom.: 28

Bravo AF: 0.0367

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2304927; hg19: chr17-75084842;