Genetic Variant SNHG29:n.379+85T>C (chr17-16439499-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000470491.8(SNHG29):n.379+85T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 533,562 control chromosomes in the GnomAD database, including 33,020 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 0.35 ( 9503 hom., cov: 33)

Exomes 𝑓: 0.34 ( 23517 hom. )

Consequence

SNHG29
ENST00000470491.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.04

Publications

10 publications found

Variant links:

COSMIC-nc: COSV58428414

Genes affected

SNHG29 (HGNC:28619): (small nucleolar RNA host gene 29)

SNHG29 links:

SNORD49B (HGNC:32721): (small nucleolar RNA, C/D box 49B)

SNORD49B links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SNHG29	NR_027158.1 link	n.162+85T>C	intron_variant	Intron 2 of 3
SNHG29	NR_027159.1 link	n.428+85T>C	intron_variant	Intron 1 of 3
SNHG29	NR_027160.1 link	n.429-82T>C	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG29	ENST00000470491.8 link	n.379+85T>C	intron_variant	Intron 1 of 2	1
SNHG29	ENST00000475953.6 link	n.378+85T>C	intron_variant	Intron 1 of 4	1
SNHG29	ENST00000481027.5 link	n.95-29T>C	intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52575

AN:

152038

Hom.:

9496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.233

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.328

GnomAD2 exomes

AF:

0.335

AC:

83851

AN:

250602

AF XY:

0.334

show subpopulations

Gnomad AFR exome

AF:

0.283

Gnomad AMR exome

AF:

0.294

Gnomad ASJ exome

AF:

0.433

Gnomad EAS exome

AF:

0.225

Gnomad FIN exome

AF:

0.432

Gnomad NFE exome

AF:

0.366

Gnomad OTH exome

AF:

0.355

GnomAD4 exome

AF:

0.343

AC:

130748

AN:

381406

Hom.:

23517

Cov.:

AF XY:

0.338

AC XY:

73426

AN XY:

217050

show subpopulations

African (AFR)

AF:

0.288

AC:

3025

AN:

10496

American (AMR)

AF:

0.293

AC:

10639

AN:

36290

Ashkenazi Jewish (ASJ)

AF:

0.430

AC:

5052

AN:

11740

East Asian (EAS)

AF:

0.224

AC:

2947

AN:

13160

South Asian (SAS)

AF:

0.261

AC:

17393

AN:

66758

European-Finnish (FIN)

AF:

0.431

AC:

13783

AN:

31946

Middle Eastern (MID)

AF:

0.353

AC:

1007

AN:

2854

European-Non Finnish (NFE)

AF:

0.371

AC:

71018

AN:

191492

Other (OTH)

AF:

0.353

AC:

5884

AN:

16670

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

5598

11196

16793

22391

27989

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

522

1044

1566

2088

2610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.346

AC:

52609

AN:

152156

Hom.:

9503

Cov.:

AF XY:

0.346

AC XY:

25725

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.290

AC:

12058

AN:

41510

American (AMR)

AF:

0.333

AC:

5089

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

1579

AN:

3464

East Asian (EAS)

AF:

0.232

AC:

1204

AN:

5180

South Asian (SAS)

AF:

0.255

AC:

1232

AN:

4828

European-Finnish (FIN)

AF:

0.436

AC:

4613

AN:

10586

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.379

AC:

25793

AN:

67990

Other (OTH)

AF:

0.330

AC:

697

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1752

3504

5255

7007

8759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

516

1032

1548

2064

2580

<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:

0.373

Hom.:

2419

Bravo

AF:

0.334

Asia WGS

AF:

0.225

AC:

784

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.19

(source)

DANN

Benign

0.48

PhyloP100

-4.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over