Genetic Variant RPL23:c.341-15_341-11dupATTTT (chr17-38850224-A-AAAAAT) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_000978.4(RPL23):c.341-15_341-11dupATTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000599 in 1,586,396 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 3 hom., cov: 32)

Exomes 𝑓: 0.00032 ( 5 hom. )

Consequence

RPL23
NM_000978.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0150

Publications

0 publications found

Variant links:

Genes affected

RPL23 (HGNC:10316): (ribosomal protein L23) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L14P family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as rpL17 because the encoded protein shares amino acid identity with ribosomal protein L17 from Saccharomyces cerevisiae; however, its official symbol is RPL23. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

RPL23 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP6

Variant 17-38850224-A-AAAAAT is Benign according to our data. Variant chr17-38850224-A-AAAAAT is described in ClinVar as Likely_benign. ClinVar VariationId is 1971298.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 488 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000978.4. 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
	RPL23	NM_000978.4	MANE Select	c.341-15_341-11dupATTTT		intron	N/A	NP_000969.1	P62829

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RPL23	ENST00000479035.7	TSL:1 MANE Select	c.341-15_341-11dupATTTT	intron	N/A	ENSP00000420311.2	P62829
RPL23	ENST00000584912.5	TSL:1	n.2631_2635dupATTTT	non_coding_transcript_exon	Exon 3 of 3
RPL23	ENST00000577407.5	TSL:2	c.104_108dupATTTT	3_prime_UTR	Exon 4 of 4	ENSP00000462773.1	J3KT29

Frequencies

GnomAD3 genomes

AF:

0.00313

AC:

476

AN:

152062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0105

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.00143

GnomAD2 exomes

AF:

0.000657

AC:

152

AN:

231182

AF XY:

0.000499

show subpopulations

Gnomad AFR exome

AF:

0.00786

Gnomad AMR exome

AF:

0.000502

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000602

Gnomad FIN exome

AF:

0.0000946

Gnomad NFE exome

AF:

0.000131

Gnomad OTH exome

AF:

0.000181

GnomAD4 exome

AF:

0.000322

AC:

462

AN:

1434216

Hom.:

Cov.:

AF XY:

0.000317

AC XY:

226

AN XY:

713496

show subpopulations

African (AFR)

AF:

0.00868

AC:

275

AN:

31686

American (AMR)

AF:

0.000698

AC:

AN:

40108

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25298

East Asian (EAS)

AF:

0.00

AC:

AN:

39280

South Asian (SAS)

AF:

0.0000863

AC:

AN:

81144

European-Finnish (FIN)

AF:

0.0000947

AC:

AN:

52776

Middle Eastern (MID)

AF:

0.000230

AC:

AN:

4346

European-Non Finnish (NFE)

AF:

0.0000963

AC:

106

AN:

1100540

Other (OTH)

AF:

0.000678

AC:

AN:

59038

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

111

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:

0.00321

AC:

488

AN:

152180

Hom.:

Cov.:

AF XY:

0.00316

AC XY:

235

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0107

AC:

446

AN:

41494

American (AMR)

AF:

0.00151

AC:

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5190

South Asian (SAS)

AF:

0.000622

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000176

AC:

AN:

68022

Other (OTH)

AF:

0.00142

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

113

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.000109

Hom.:

Asia WGS

AF:

0.000578

AC:

AN:

3476

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.015

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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17-38850224-AAAAATAAAAT-AAAAATAAAATAAAAT

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