15-55183197-G-A

Variant names:

• chr15-55183197-G-A
• rs8035625
• NM_016304.3:c.418+118C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 2 publications found

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016304.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSL24D1	NM_016304.3	MANE Select	c.418+118C>T		intron	N/A	NP_057388.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSL24D1	ENST00000260443.9	TSL:1 MANE Select	c.418+118C>T		intron	N/A	ENSP00000260443.4
	RSL24D1	ENST00000677730.1		c.422+114C>T		intron	N/A	ENSP00000503411.1
	RSL24D1	ENST00000677147.1		c.427+118C>T		intron	N/A	ENSP00000503127.1

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

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

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

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: 39 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9522 AN: 67942

Other (OTH) AF: 0.152 AC: 320 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.45
PhyloP100		-0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8035625; hg19: chr15-55475395;