dbSNP rs8035625: RSL24D1:c.418+118C>T (chr15-55183197-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016304.3(RSL24D1):c.418+118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 683,214 control chromosomes in the GnomAD database, including 8,292 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 0.17 ( 2566 hom., cov: 32)

Exomes 𝑓: 0.14 ( 5726 hom. )

Consequence

RSL24D1
NM_016304.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.813

Publications

2 publications found

Variant links:

Genes affected

RSL24D1 (HGNC:18479): (ribosomal L24 domain containing 1) This gene encodes a protein sharing a low level of sequence similarity with human ribosomal protein L24. Although this gene has been referred to as RPL24, L30, and 60S ribosomal protein L30 isolog in the sequence databases, it is distinct from the human genes officially named RPL24 (which itself has been referred to as ribosomal protein L30) and RPL30. The protein encoded by this gene localizes to the nucleolus and is thought to play a role in the biogenesis of the 60S ribosomal subunit. The precise function of this gene is currently unknown. This gene utilizes alternative polyadenylation signals and has multiple pseudogenes. [provided by RefSeq, Jul 2012]

RSL24D1 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSL24D1	NM_016304.3 link	c.418+118C>T		intron_variant	Intron 5 of 5	ENST00000260443.9	NP_057388.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSL24D1	ENST00000260443.9 link	c.418+118C>T		intron_variant	Intron 5 of 5	1	NM_016304.3	ENSP00000260443.4

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26216

AN:

151774

Hom.:

2557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.121

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.153

GnomAD4 exome

AF:

0.143

AC:

75885

AN:

531322

Hom.:

5726

AF XY:

0.144

AC XY:

39949

AN XY:

277508

show subpopulations

African (AFR)

AF:

0.273

AC:

3518

AN:

12896

American (AMR)

AF:

0.0938

AC:

1580

AN:

16838

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

1557

AN:

14042

East Asian (EAS)

AF:

0.0951

AC:

2809

AN:

29536

South Asian (SAS)

AF:

0.170

AC:

6990

AN:

41044

European-Finnish (FIN)

AF:

0.137

AC:

5934

AN:

43272

Middle Eastern (MID)

AF:

0.158

AC:

331

AN:

2094

European-Non Finnish (NFE)

AF:

0.143

AC:

49059

AN:

344134

Other (OTH)

AF:

0.150

AC:

4107

AN:

27466

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

3099

6199

9298

12398

15497

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

916

1832

2748

3664

4580

<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:

0.173

AC:

26251

AN:

151892

Hom.:

2566

Cov.:

AF XY:

0.171

AC XY:

12682

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.268

AC:

11090

AN:

41394

American (AMR)

AF:

0.116

AC:

1771

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

398

AN:

3466

East Asian (EAS)

AF:

0.121

AC:

629

AN:

5178

South Asian (SAS)

AF:

0.180

AC:

865

AN:

4808

European-Finnish (FIN)

AF:

0.131

AC:

1377

AN:

10536

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.140

AC:

9522

AN:

67942

Other (OTH)

AF:

0.152

AC:

320

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1084

2167

3251

4334

5418

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

286

572

858

1144

1430

<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:

0.165

Hom.:

404

Bravo

AF:

0.174

Asia WGS

AF:

0.182

AC:

633

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.48

(source)

DANN

Benign

0.45

PhyloP100

-0.81

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