Genetic Variant 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:

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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=-0.9).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152551.4. 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
	SNRNP48	NM_152551.4	MANE Select	c.*410T>C		3_prime_UTR	Exon 9 of 9	NP_689764.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SNRNP48	ENST00000342415.6	TSL:1 MANE Select	c.*410T>C	3_prime_UTR	Exon 9 of 9	ENSP00000339834.4	Q6IEG0-1
SNRNP48	ENST00000864978.1		c.*410T>C	3_prime_UTR	Exon 9 of 9	ENSP00000535037.1
SNRNP48	ENST00000864979.1		c.*410T>C	3_prime_UTR	Exon 8 of 8	ENSP00000535038.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over