20-38422170-C-T

Variant names:

• chr20-38422170-C-T
• rs3752278
• ENST00000701521.2:n.772G>A

Variant summary

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

The ENST00000414142.5(SNHG17):​n.630G>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 0.231 in 152,288 control chromosomes in the GnomAD database, including 5,108 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 (5104 hom., cov: 32)
  • Exomes 𝑓: 0.25 (4 hom.)
• Consequence: SNHG17 ENST00000414142.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 12 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414142.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG17	NR_185934.1	MANE Select	n.772G>A		non_coding_transcript_exon	Exon 6 of 8
	SNHG17	NR_015366.6		n.602G>A		non_coding_transcript_exon	Exon 6 of 8
	SNHG17	NR_027241.4		n.654G>A		non_coding_transcript_exon	Exon 5 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG17	ENST00000701521.2	MANE Select	n.772G>A		non_coding_transcript_exon	Exon 6 of 8
	SNHG17	ENST00000413755.7	TSL:3	n.670G>A		non_coding_transcript_exon	Exon 5 of 7
	SNHG17	ENST00000414142.5	TSL:2	n.630G>A		non_coding_transcript_exon	Exon 7 of 8

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35102 AN: 152060 Hom.: 5084 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.245 AC: 27 AN: 110 Hom.: 4 Cov.: 0 AF XY: 0.250 AC XY: 21 AN XY: 84

African (AFR) AF: 0.400 AC: 4 AN: 10

American (AMR) AF: 0.00 AC: 0 AN: 2

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: 0.300 AC: 6 AN: 20

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.236 AC: 17 AN: 72

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.231 AC: 35167 AN: 152178 Hom.: 5104 Cov.: 32 AF XY: 0.230 AC XY: 17119 AN XY: 74420

African (AFR) AF: 0.415 AC: 17238 AN: 41512

American (AMR) AF: 0.163 AC: 2498 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3470

East Asian (EAS) AF: 0.0963 AC: 498 AN: 5174

South Asian (SAS) AF: 0.196 AC: 944 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10598

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

European-Non Finnish (NFE) AF: 0.161 AC: 10936 AN: 67982

Other (OTH) AF: 0.213 AC: 451 AN: 2116

Alfa AF: 0.185 Hom.: 1611

Bravo AF: 0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

Other links and lift over

dbSNP: rs3752278; hg19: chr20-37050817;