rs11645213

Variant names:

• chr16-11849067-C-A
• rs11645213
• NM_015659.3:c.245+1212G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-11849067-C-A
• chr16-11849067-C-G
• chr16-11849067-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RSL1D1	NM_015659.3	c.245+1212G>T		intron_variant	Intron 2 of 8	ENST00000571133.6	NP_056474.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSL1D1	ENST00000571133.6	c.245+1212G>T		intron_variant	Intron 2 of 8	1	NM_015659.3	ENSP00000460871.1

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

African (AFR) AF: 0.164 AC: 6797 AN: 41426

American (AMR) AF: 0.479 AC: 7294 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1892 AN: 3464

East Asian (EAS) AF: 0.189 AC: 976 AN: 5158

South Asian (SAS) AF: 0.365 AC: 1762 AN: 4822

European-Finnish (FIN) AF: 0.495 AC: 5205 AN: 10520

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39676 AN: 67932

Other (OTH) AF: 0.476 AC: 999 AN: 2098

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
PhyloP100		0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs11645213; hg19: chr16-11942924;