15-55183197-G-A

Position:

• chr15-55183197-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000260443.9(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 ENST00000260443.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
RSL24D1	NM_016304.3	c.418+118C>T		intron_variant		ENST00000260443.9	NP_057388.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSL24D1	ENST00000260443.9	c.418+118C>T		intron_variant		1	NM_016304.3	ENSP00000260443	P4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26216 AN: 151774 Hom.: 2557 Cov.: 32

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

Gnomad4 AFR exome AF: 0.273

Gnomad4 AMR exome AF: 0.0938

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.0951

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.173 AC: 26251 AN: 151892 Hom.: 2566 Cov.: 32 AF XY: 0.171 AC XY: 12682 AN XY: 74250

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.152

Alfa AF: 0.162 Hom.: 372

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
DANN	Benign	0.45

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

LitVar

Other links and lift over

dbSNP: rs8035625; hg19: chr15-55475395;