dbSNP rs10498025: SNHG31:n.350+50427A>G (chr2-214884532-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000607412.2(SNHG31):n.350+50427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,902 control chromosomes in the GnomAD database, including 3,642 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 0.21 ( 3642 hom., cov: 32)

Consequence

SNHG31
ENST00000607412.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.60

Publications

7 publications found

Variant links:

Genes affected

SNHG31 (HGNC:54196): (small nucleolar RNA host gene 31)

SNHG31 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG31	NR_110292.1 link	n.321+50427A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG31	ENST00000607412.2 link	n.350+50427A>G	intron_variant	Intron 2 of 3	2
SNHG31	ENST00000655899.1 link	n.369+50427A>G	intron_variant	Intron 2 of 3
SNHG31	ENST00000664818.2 link	n.451+50427A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32552

AN:

151782

Hom.:

3644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.346

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.225

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

GnomAD4 genome

AF:

0.214

AC:

32538

AN:

151902

Hom.:

3642

Cov.:

AF XY:

0.216

AC XY:

16012

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.153

AC:

6361

AN:

41472

American (AMR)

AF:

0.178

AC:

2714

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

856

AN:

3470

East Asian (EAS)

AF:

0.219

AC:

1125

AN:

5140

South Asian (SAS)

AF:

0.345

AC:

1651

AN:

4792

European-Finnish (FIN)

AF:

0.238

AC:

2513

AN:

10542

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.243

AC:

16520

AN:

67906

Other (OTH)

AF:

0.222

AC:

468

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1233

2466

3699

4932

6165

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.225

Hom.:

2163

Bravo

AF:

0.205

Asia WGS

AF:

0.251

AC:

874

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.33

(source)

DANN

Benign

0.50

PhyloP100

-2.6

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over