Variant rs2757598 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SNRNP48	NM_152551.4 linkuse as main transcript	c.*930C>A		3_prime_UTR_variant	9/9	ENST00000342415.6
SNRNP48	XM_011514312.4 linkuse as main transcript	c.*930C>A		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNRNP48	ENST00000342415.6 linkuse as main transcript	c.*930C>A		3_prime_UTR_variant	9/9	1	NM_152551.4	P1	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:

GnomAD4 genome

AF:

0.696

AC:

105800

AN:

151988

Hom.:

37282

Cov.:

AF XY:

0.696

AC XY:

51678

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.816

Gnomad4 AMR

AF:

0.695

Gnomad4 ASJ

AF:

0.757

Gnomad4 EAS

AF:

0.604

Gnomad4 SAS

AF:

0.663

Gnomad4 FIN

AF:

0.666

Gnomad4 NFE

AF:

0.635

Gnomad4 OTH

AF:

0.686

Alfa

AF:

0.644

Hom.:

50947

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

DANN

Benign

0.49

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over