dbSNP rs2757598: SNRNP48:c.*930C>A (chr6-7609803-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_152551.4(SNRNP48):c.*930C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,988 control chromosomes in the GnomAD database, including 37,282 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 0.70 ( 37282 hom., cov: 31)

Failed GnomAD Quality Control

Consequence

SNRNP48
NM_152551.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0270

Publications

5 publications found

Variant links:

Genes affected

SNRNP48 (HGNC:21368): (small nuclear ribonucleoprotein U11/U12 subunit 48) Predicted to enable metal ion binding activity. Predicted to be involved in RNA splicing. Located in cytosol and nucleoplasm. Part of U12-type spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

SNRNP48 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNRNP48	NM_152551.4 link	c.*930C>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000342415.6	NP_689764.3	Q6IEG0-1
SNRNP48	XM_011514312.4 link	c.*930C>A		3_prime_UTR_variant	Exon 9 of 9		XP_011512614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNRNP48	ENST00000342415.6 link	c.*930C>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_152551.4	ENSP00000339834.4		Q6IEG0-1

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105693

AN:

151872

Hom.:

37224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.816

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.695

Gnomad ASJ

AF:

0.757

Gnomad EAS

AF:

0.605

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.666

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.635

Gnomad OTH

AF:

0.683

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.696

AC:

105800

AN:

151988

Hom.:

37282

Cov.:

AF XY:

0.696

AC XY:

51678

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.816

AC:

33826

AN:

41430

American (AMR)

AF:

0.695

AC:

10608

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.757

AC:

2622

AN:

3464

East Asian (EAS)

AF:

0.604

AC:

3119

AN:

5160

South Asian (SAS)

AF:

0.663

AC:

3190

AN:

4810

European-Finnish (FIN)

AF:

0.666

AC:

7039

AN:

10568

Middle Eastern (MID)

AF:

0.684

AC:

201

AN:

294

European-Non Finnish (NFE)

AF:

0.635

AC:

43139

AN:

67980

Other (OTH)

AF:

0.686

AC:

1441

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1609

3219

4828

6438

8047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.653

Hom.:

123807

Bravo

AF:

0.701

Asia WGS

AF:

0.669

AC:

2331

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.8

(source)

DANN

Benign

0.49

PhyloP100

0.027

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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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rs2757598

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