Genetic Variant ENST00000470491.8:n.379+85T>A (chr17-16439499-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000470491.8(SNHG29):n.379+85T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000262 in 381,466 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000026 ( 0 hom. )

Consequence

SNHG29
ENST00000470491.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.04

Publications

10 publications found

Variant links:

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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000262

AC:

AN:

381466

Hom.:

Cov.:

AF XY:

0.00000461

AC XY:

AN XY:

217090

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10496

American (AMR)

AF:

0.00

AC:

AN:

36290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11742

East Asian (EAS)

AF:

0.00

AC:

AN:

13160

South Asian (SAS)

AF:

0.00

AC:

AN:

66758

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31968

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2854

European-Non Finnish (NFE)

AF:

0.00000522

AC:

AN:

191526

Other (OTH)

AF:

0.00

AC:

AN:

16672

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.15

(source)

DANN

Benign

0.70

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over