17-42998447-TG-T

Position:

• chr17-42998447-TG-T

Variant summary

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

The NM_000988.5(RPL27):​c.-25del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.94 (67452 hom., cov: 0)
  • Exomes 𝑓: 0.99 (64171 hom.)
• Consequence: RPL27 NM_000988.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.418

Genes affected

RPL27 (HGNC:10328): (ribosomal protein L27) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the L27e family of ribosomal proteins and a component of the 60S subunit. A splice site mutation in this gene has been identified in a Diamond-Blackfan anemia (DBA) patient. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Mar 2017]

LOC124904006 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-42998447-TG-T is Benign according to our data. Variant chr17-42998447-TG-T is described in ClinVar as [Benign]. Clinvar id is 1270607.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL27	NM_000988.5	c.-25del		5_prime_UTR_variant	1/5	ENST00000253788.12	NP_000979.1
LOC124904006	XR_007065759.1	n.1152del		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL27	ENST00000253788.12	c.-25del		5_prime_UTR_variant	1/5	1	NM_000988.5	ENSP00000253788	P1

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142420 AN: 152062 Hom.: 67411 Cov.: 0

Gnomad AFR AF: 0.779

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.956

GnomAD4 exome AF: 0.994 AC: 129039 AN: 129866 Hom.: 64171 Cov.: 0 AF XY: 0.995 AC XY: 69935 AN XY: 70314

Gnomad4 AFR exome AF: 0.781

Gnomad4 AMR exome AF: 0.982

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.999

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.999

Gnomad4 OTH exome AF: 0.986

GnomAD4 genome AF: 0.936 AC: 142515 AN: 152180 Hom.: 67452 Cov.: 0 AF XY: 0.938 AC XY: 69801 AN XY: 74400

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.980

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.957

Alfa AF: 0.958 Hom.: 8571

Bravo AF: 0.922

Asia WGS AF: 0.986 AC: 3429 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs11305686; hg19: chr17-41150464;