dbSNP rs6744811: SNHG31:n.233+2152A>C (chr2-214812584-A-C) – 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.233+2152A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,908 control chromosomes in the GnomAD database, including 9,110 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 0.34 ( 9110 hom., cov: 30)

Consequence

SNHG31
ENST00000607412.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.800

Publications

4 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG31	NR_110292.1 link	n.204+2152A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG31	ENST00000607412.2 link	n.233+2152A>C	intron_variant	Intron 1 of 3	2
SNHG31	ENST00000655899.1 link	n.252+2152A>C	intron_variant	Intron 1 of 3
SNHG31	ENST00000664818.2 link	n.334+2152A>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51055

AN:

151790

Hom.:

9101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.344

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

GnomAD4 genome

AF:

0.336

AC:

51085

AN:

151908

Hom.:

9110

Cov.:

AF XY:

0.340

AC XY:

25216

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.213

AC:

8827

AN:

41418

American (AMR)

AF:

0.388

AC:

5926

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.437

AC:

1517

AN:

3470

East Asian (EAS)

AF:

0.355

AC:

1831

AN:

5164

South Asian (SAS)

AF:

0.410

AC:

1973

AN:

4818

European-Finnish (FIN)

AF:

0.410

AC:

4307

AN:

10512

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.376

AC:

25552

AN:

67932

Other (OTH)

AF:

0.343

AC:

725

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1696

3392

5089

6785

8481

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

514

1028

1542

2056

2570

<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:

0.358

Hom.:

16400

Bravo

AF:

0.325

Asia WGS

AF:

0.371

AC:

1290

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.2

(source)

DANN

Benign

0.69

PhyloP100

0.80

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