rs11645213

chr16-11849067-C-Achr16-11849067-C-Gchr16-11849067-C-T

Variant summary

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

The NM_015659.3(RSL1D1):c.245+1212G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,854 control chromosomes in the GnomAD database, including 16,744 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 0.43 (16744 hom., cov: 31)
• Consequence: RSL1D1 NM_015659.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

RSL1D1 (HGNC:24534): (ribosomal L1 domain containing 1) Enables mRNA 3'-UTR binding activity and mRNA 5'-UTR binding activity. Involved in regulation of apoptotic process and regulation of cellular senescence. Acts upstream of or within regulation of protein localization. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSL1D1	NM_015659.3	c.245+1212G>T		intron_variant		ENST00000571133.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSL1D1	ENST00000571133.6	c.245+1212G>T		intron_variant		1	NM_015659.3	P1

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65273 AN: 151736 Hom.: 16750 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.481

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.430 AC: 65268 AN: 151854 Hom.: 16744 Cov.: 31 AF XY: 0.424 AC XY: 31496 AN XY: 74232

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.476

Alfa AF: 0.378 Hom.: 1233

Bravo AF: 0.416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs11645213; hg19: chr16-11942924;