11-119018686-G-GAGA

Variant names:

• chr11-119018686-G-GAGA
• rs1555188820
• ENST00000527853.1:n.5_6insTCT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000527853.1(RPS25):​n.5_6insTCT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.052 (432 hom., cov: 0)
  • Exomes 𝑓: 0.020 (641 hom.)
• Consequence: RPS25 ENST00000527853.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.225

Genes affected

RPS25 (HGNC:10413): (ribosomal protein S25) 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 40S subunit. The protein belongs to the S25E 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]

TRAPPC4 (HGNC:19943): (trafficking protein particle complex subunit 4) Involved in autophagy and endoplasmic reticulum to Golgi vesicle-mediated transport. Part of TRAPP complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-119018686-G-GAGA is Benign according to our data. Variant chr11-119018686-G-GAGA is described in ClinVar as [Benign]. Clinvar id is 1250697.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC4	NM_016146.6	c.-110_-109insAGA		upstream_gene_variant		ENST00000533632.6	NP_057230.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAPPC4	ENST00000533632.6	c.-110_-109insAGA		upstream_gene_variant		1	NM_016146.6	ENSP00000436005.1

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7869 AN: 151622 Hom.: 431 Cov.: 0

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.00289

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0318

GnomAD4 exome AF: 0.0197 AC: 19837 AN: 1004698 Hom.: 641 Cov.: 14 AF XY: 0.0201 AC XY: 10192 AN XY: 508174

Gnomad4 AFR exome AF: 0.133

Gnomad4 AMR exome AF: 0.0168

Gnomad4 ASJ exome AF: 0.00228

Gnomad4 EAS exome AF: 0.0405

Gnomad4 SAS exome AF: 0.0424

Gnomad4 FIN exome AF: 0.0435

Gnomad4 NFE exome AF: 0.0117

Gnomad4 OTH exome AF: 0.0244

GnomAD4 genome AF: 0.0520 AC: 7889 AN: 151740 Hom.: 432 Cov.: 0 AF XY: 0.0537 AC XY: 3986 AN XY: 74166

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.00289

Gnomad4 EAS AF: 0.0569

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.0123

Gnomad4 OTH AF: 0.0314

Alfa AF: 0.00432 Hom.: 2

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 30, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555188820; hg19: chr11-118889396;