dbSNP rs1539537: SNRNP48:c.*410T>C (chr6-7609283-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 NM_152551.4(SNRNP48):c.*410T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,602 control chromosomes in the GnomAD database, including 38,666 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 0.71 ( 38514 hom., cov: 32)

Exomes 𝑓: 0.72 ( 152 hom. )

Consequence

SNRNP48
NM_152551.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.351

Publications

4 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:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNRNP48	NM_152551.4 link	c.*410T>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000342415.6	NP_689764.3	Q6IEG0-1
SNRNP48	XM_011514312.4 link	c.*410T>C		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.*410T>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_152551.4	ENSP00000339834.4		Q6IEG0-1
SNRNP48	ENST00000496946.1 link	n.*77T>C		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.706

AC:

107219

AN:

151932

Hom.:

38452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.848

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.756

Gnomad EAS

AF:

0.607

Gnomad SAS

AF:

0.664

Gnomad FIN

AF:

0.666

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.688

GnomAD4 exome

AF:

0.723

AC:

399

AN:

552

Hom.:

152

Cov.:

AF XY:

0.719

AC XY:

220

AN XY:

306

show subpopulations

African (AFR)

AF:

0.833

AC:

AN:

American (AMR)

AF:

0.636

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.864

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.976

AC:

121

AN:

124

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.616

AC:

207

AN:

336

Other (OTH)

AF:

0.818

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.706

AC:

107331

AN:

152050

Hom.:

38514

Cov.:

AF XY:

0.705

AC XY:

52404

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.848

AC:

35204

AN:

41494

American (AMR)

AF:

0.698

AC:

10669

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.756

AC:

2623

AN:

3470

East Asian (EAS)

AF:

0.607

AC:

3139

AN:

5174

South Asian (SAS)

AF:

0.665

AC:

3200

AN:

4814

European-Finnish (FIN)

AF:

0.666

AC:

7020

AN:

10544

Middle Eastern (MID)

AF:

0.690

AC:

203

AN:

294

European-Non Finnish (NFE)

AF:

0.636

AC:

43204

AN:

67968

Other (OTH)

AF:

0.691

AC:

1457

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1596

3193

4789

6386

7982

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

816

1632

2448

3264

4080

<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:

0.677

Hom.:

12096

Bravo

AF:

0.712

Asia WGS

AF:

0.673

AC:

2342

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.37

(source)

DANN

Benign

0.40

PhyloP100

-0.35

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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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