13-27256416-C-CT

Variant names:

• chr13-27256416-C-CT
• rs749953441
• NM_000982.4:c.394-11dupT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_000982.4(RPL21):​c.394-11dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,546,062 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00059 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0011 (0 hom.)
• Consequence: RPL21 NM_000982.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.21

Genes affected

RPL21 (HGNC:10313): (ribosomal protein L21) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L21E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 13-27256416-C-CT is Benign according to our data. Variant chr13-27256416-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 1988640.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 89 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL21	NM_000982.4	c.394-11dupT		intron_variant	Intron 5 of 5	ENST00000311549.11	NP_000973.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL21	ENST00000311549.11	c.394-20_394-19insT		intron_variant	Intron 5 of 5	1	NM_000982.4	ENSP00000346027.4

Frequencies

GnomAD3 genomes AF: 0.000589 AC: 89 AN: 151222 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00204

Gnomad ASJ AF: 0.00289

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000628

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000354

Gnomad OTH AF: 0.00338

GnomAD4 exome AF: 0.00114 AC: 1592 AN: 1394724 Hom.: 0 Cov.: 25 AF XY: 0.00112 AC XY: 783 AN XY: 697172

Gnomad4 AFR exome AF: 0.000688

Gnomad4 AMR exome AF: 0.00120

Gnomad4 ASJ exome AF: 0.00278

Gnomad4 EAS exome AF: 0.000282

Gnomad4 SAS exome AF: 0.000840

Gnomad4 FIN exome AF: 0.000114

Gnomad4 NFE exome AF: 0.00113

Gnomad4 OTH exome AF: 0.00184

GnomAD4 genome AF: 0.000588 AC: 89 AN: 151338 Hom.: 1 Cov.: 32 AF XY: 0.000528 AC XY: 39 AN XY: 73920

Gnomad4 AFR AF: 0.000267

Gnomad4 AMR AF: 0.00204

Gnomad4 ASJ AF: 0.00289

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000629

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000354

Gnomad4 OTH AF: 0.00334

Bravo AF: 0.000574

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 20, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

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: rs749953441; hg19: chr13-27830553;