rs1739652

chr20-38420312-A-Gchr20-38420312-A-T

Variant summary

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

The ENST00000654008.2(SNHG17):n.1195+221T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,138 control chromosomes in the GnomAD database, including 5,087 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 0.23 (5087 hom., cov: 32)
• Consequence: SNHG17 ENST00000654008.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

Genes affected

SNHG17 (HGNC:48600): (small nucleolar RNA host gene 17)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG17	ENST00000654008.2	n.1195+221T>C		intron_variant, non_coding_transcript_variant
SNHG17	ENST00000658076.2	n.1389T>C		non_coding_transcript_exon_variant	7/7
SNHG17	ENST00000662982.3	n.1228T>C		non_coding_transcript_exon_variant	7/7

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35064 AN: 152020 Hom.: 5067 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.215

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.231 AC: 35129 AN: 152138 Hom.: 5087 Cov.: 32 AF XY: 0.230 AC XY: 17093 AN XY: 74396

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0967

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.213

Alfa AF: 0.172 Hom.: 2567

Bravo AF: 0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1739652; hg19: chr20-37048959;