Genetic Variant SNRPB:c.155+301G>A (chr20-2467306-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_003091.4(SNRPB):c.155+301G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 365,336 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: 32)

Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

SNRPB
NM_003091.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.728

Publications

3 publications found

Variant links:

Genes affected

SNRPB (HGNC:11153): (small nuclear ribonucleoprotein polypeptides B and B1) The protein encoded by this gene is one of several nuclear proteins that are found in common among U1, U2, U4/U6, and U5 small ribonucleoprotein particles (snRNPs). These snRNPs are involved in pre-mRNA splicing, and the encoded protein may also play a role in pre-mRNA splicing or snRNP structure. Autoantibodies from patients with systemic lupus erythematosus frequently recognize epitopes on the encoded protein. Two transcript variants encoding different isoforms (B and B') have been found for this gene. [provided by RefSeq, Jul 2008]

SNRPB Gene-Disease associations (from GenCC):

cerebrocostomandibular syndrome
Inheritance: AD, SD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, PanelApp Australia

SNRPB links:

ENSG00000256566 (HGNC:):

ENSG00000256566 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003091.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPB	NM_003091.4	MANE Select	c.155+301G>A		intron	N/A	NP_003082.1	Q66K91
	SNRPB	NM_198216.2		c.155+301G>A		intron	N/A	NP_937859.1	P14678-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SNRPB	ENST00000381342.7	TSL:1 MANE Select	c.155+301G>A	intron	N/A	ENSP00000370746.3	P14678-2
SNRPB	ENST00000438552.6	TSL:1	c.155+301G>A	intron	N/A	ENSP00000412566.2	P14678-1
ENSG00000256566	ENST00000461548.1	TSL:5	n.*124G>A	non_coding_transcript_exon	Exon 7 of 7	ENSP00000456213.1	F5H5K5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000740

AC:

AN:

135074

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000188

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000547

AC:

AN:

365336

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

203930

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10956

American (AMR)

AF:

0.00

AC:

AN:

28994

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13528

East Asian (EAS)

AF:

0.00

AC:

AN:

14736

South Asian (SAS)

AF:

0.00

AC:

AN:

60296

European-Finnish (FIN)

AF:

0.00

AC:

AN:

16372

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3060

European-Non Finnish (NFE)

AF:

0.00000503

AC:

AN:

198938

Other (OTH)

AF:

0.0000542

AC:

AN:

18456

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

(source)

DANN

Benign

0.95

PhyloP100

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over