dbSNP rs17084051: ENSG00000282278:c.1018-53511C>A (chr4-54221414-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 ENST00000507166.5(ENSG00000282278):c.1018-53511C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 534,414 control chromosomes in the GnomAD database, including 13,463 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 0.25 ( 5148 hom., cov: 32)

Exomes 𝑓: 0.20 ( 8315 hom. )

Consequence

ENSG00000282278
ENST00000507166.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.57

Publications

26 publications found

Variant links:

Genes affected

ENSG00000282278 (HGNC:):

ENSG00000282278 links:

RPL22P13 (HGNC:36352): (ribosomal protein L22 pseudogene 13)

RPL22P13 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000507166.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.53).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507166.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282278	ENST00000507166.5	TSL:2	c.1018-53511C>A		intron	N/A	ENSP00000423325.1	A0A0B4J203
	RPL22P13	ENST00000493291.1	TSL:6	n.289C>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38146

AN:

151824

Hom.:

5141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.221

GnomAD4 exome

AF:

0.201

AC:

76998

AN:

382472

Hom.:

8315

Cov.:

AF XY:

0.199

AC XY:

41062

AN XY:

206162

show subpopulations

African (AFR)

AF:

0.299

AC:

2991

AN:

9990

American (AMR)

AF:

0.347

AC:

5313

AN:

15322

Ashkenazi Jewish (ASJ)

AF:

0.0971

AC:

1215

AN:

12510

East Asian (EAS)

AF:

0.167

AC:

3749

AN:

22398

South Asian (SAS)

AF:

0.222

AC:

9312

AN:

41940

European-Finnish (FIN)

AF:

0.200

AC:

7457

AN:

37290

Middle Eastern (MID)

AF:

0.175

AC:

565

AN:

3226

European-Non Finnish (NFE)

AF:

0.193

AC:

42184

AN:

219048

Other (OTH)

AF:

0.203

AC:

4212

AN:

20748

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

2483

4965

7448

9930

12413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.251

AC:

38197

AN:

151942

Hom.:

5148

Cov.:

AF XY:

0.251

AC XY:

18668

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.326

AC:

13493

AN:

41390

American (AMR)

AF:

0.331

AC:

5046

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

351

AN:

3468

East Asian (EAS)

AF:

0.198

AC:

1025

AN:

5170

South Asian (SAS)

AF:

0.255

AC:

1228

AN:

4820

European-Finnish (FIN)

AF:

0.207

AC:

2181

AN:

10554

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.209

AC:

14236

AN:

67990

Other (OTH)

AF:

0.218

AC:

460

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1432

2864

4296

5728

7160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.219

Hom.:

17721

Bravo

AF:

0.264

Asia WGS

AF:

0.253

AC:

882

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

2.3

(source)

DANN

Benign

0.55

PhyloP100

1.6

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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