rs1739652

Variant names:

• chr20-38420312-A-G
• rs1739652
• ENST00000658076.3:n.1395T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-38420312-A-G
• chr20-38420312-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658076.3(SNHG17):​n.1395T>C 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 0.231 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 ENST00000658076.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG17	ENST00000658076.3	n.1395T>C		non_coding_transcript_exon_variant	Exon 7 of 7
SNHG17	ENST00000662982.4	n.1253T>C		non_coding_transcript_exon_variant	Exon 7 of 7
SNHG17	ENST00000654008.2	n.1195+221T>C		intron_variant	Intron 8 of 8
SNHG17	ENST00000666549.2	n.*208T>C		downstream_gene_variant

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

African (AFR) AF: 0.415 AC: 17210 AN: 41472

American (AMR) AF: 0.163 AC: 2492 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3472

East Asian (EAS) AF: 0.0967 AC: 501 AN: 5180

South Asian (SAS) AF: 0.196 AC: 944 AN: 4822

European-Finnish (FIN) AF: 0.149 AC: 1582 AN: 10604

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10935 AN: 67992

Other (OTH) AF: 0.213 AC: 450 AN: 2110

Alfa AF: 0.195 Hom.: 4928

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
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs1739652; hg19: chr20-37048959;