18-57838630-C-T

Variant names:

• chr18-57838630-C-T
• rs576180
• ENST00000591045.1:n.155C>T

Variant summary

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

The ENST00000591045.1(RSL24D1P11):​n.155C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 557,762 control chromosomes in the GnomAD database, including 166 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 0.030 (121 hom., cov: 33)
  • Exomes 𝑓: 0.0093 (45 hom.)
• Consequence: RSL24D1P11 ENST00000591045.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.55
• Publications: 1 publications found

Genes affected

RSL24D1P11 (HGNC:37881): (ribosomal L24 domain containing 1 pseudogene 11)

ENSG00000303117 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSL24D1P11		n.57838630C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSL24D1P11	ENST00000591045.1	n.155C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000303117	ENST00000791946.1	n.354+5426C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4530 AN: 152046 Hom.: 121 Cov.: 33

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0124

Gnomad ASJ AF: 0.00404

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00539

Gnomad FIN AF: 0.00935

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00980

Gnomad OTH AF: 0.0186

GnomAD4 exome AF: 0.00927 AC: 3758 AN: 405598 Hom.: 45 Cov.: 2 AF XY: 0.00877 AC XY: 2011 AN XY: 229332

African (AFR) AF: 0.0714 AC: 792 AN: 11098

American (AMR) AF: 0.00601 AC: 214 AN: 35618

Ashkenazi Jewish (ASJ) AF: 0.00462 AC: 61 AN: 13212

East Asian (EAS) AF: 0.00 AC: 0 AN: 16206

South Asian (SAS) AF: 0.00554 AC: 366 AN: 66016

European-Finnish (FIN) AF: 0.00909 AC: 186 AN: 20460

Middle Eastern (MID) AF: 0.0182 AC: 26 AN: 1426

European-Non Finnish (NFE) AF: 0.00870 AC: 1933 AN: 222164

Other (OTH) AF: 0.00928 AC: 180 AN: 19398

GnomAD4 genome AF: 0.0298 AC: 4538 AN: 152164 Hom.: 121 Cov.: 33 AF XY: 0.0294 AC XY: 2188 AN XY: 74396

African (AFR) AF: 0.0842 AC: 3495 AN: 41488

American (AMR) AF: 0.0124 AC: 190 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00404 AC: 14 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4822

European-Finnish (FIN) AF: 0.00935 AC: 99 AN: 10586

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00978 AC: 665 AN: 68022

Other (OTH) AF: 0.0184 AC: 39 AN: 2116

Alfa AF: 0.0170 Hom.: 22

Bravo AF: 0.0319

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs576180; hg19: chr18-55505862;