Genetic Variant SNHG20:n.130G>A (chr17-77088760-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000434411.6(SNHG20):n.130G>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
ENST00000434411.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.569

Publications

5 publications found

Variant links:

Genes affected

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

SNHG20 links:

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]

SEC14L1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434411.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
SNHG20	NR_027058.1	n.118G>A	non_coding_transcript_exon	Exon 1 of 3
SEC14L1	NM_001204408.2	c.-548G>A	5_prime_UTR	Exon 1 of 20	NP_001191337.2
SEC14L1	NM_001204410.2	c.-548G>A	5_prime_UTR	Exon 1 of 19	NP_001191339.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
SNHG20	ENST00000434411.6	TSL:1	n.130G>A	non_coding_transcript_exon	Exon 1 of 3
SNHG20	ENST00000561633.5	TSL:1	n.12G>A	non_coding_transcript_exon	Exon 1 of 4
SNHG20	ENST00000564509.5	TSL:1	n.12G>A	non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0378

AC:

5629

AN:

148874

Hom.:

194

Cov.:

show subpopulations

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:

AN:

112

Hom.:

Cov.:

AF XY:

0.0581

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0222

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0378

AC:

5629

AN:

148994

Hom.:

192

Cov.:

AF XY:

0.0381

AC XY:

2771

AN XY:

72732

show subpopulations

African (AFR)

AF:

0.0123

AC:

497

AN:

40374

American (AMR)

AF:

0.0219

AC:

327

AN:

14920

Ashkenazi Jewish (ASJ)

AF:

0.0601

AC:

204

AN:

3394

East Asian (EAS)

AF:

0.210

AC:

1051

AN:

5008

South Asian (SAS)

AF:

0.0257

AC:

119

AN:

4622

European-Finnish (FIN)

AF:

0.0463

AC:

482

AN:

10410

Middle Eastern (MID)

AF:

0.0411

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0417

AC:

2794

AN:

67004

Other (OTH)

AF:

0.0397

AC:

AN:

2064

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

268

535

803

1070

1338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0394

Hom.:

Bravo

AF:

0.0367

Asia WGS

AF:

0.0920

AC:

319

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.9

(source)

DANN

Benign

0.81

PhyloP100

-0.57

PromoterAI

-0.081

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over