chr17-42999726-G-T

Variant names:

• chr17-42999726-G-T
• rs691711
• NM_000988.5:c.82-207G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000988.5(RPL27):​c.82-207G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000025 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RPL27 NM_000988.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 1 publications found

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]

RPL27 Gene-Disease associations (from GenCC):

• Diamond-Blackfan anemia 16

  Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics

LOC124904006 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000988.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL27	NM_000988.5	MANE Select	c.82-207G>T		intron	N/A	NP_000979.1	P61353
	RPL27	NM_001349921.2		c.82-207G>T		intron	N/A	NP_001336850.1	P61353
	RPL27	NM_001349922.2		c.82-207G>T		intron	N/A	NP_001336851.1	P61353

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL27	ENST00000253788.12	TSL:1 MANE Select	c.82-207G>T		intron	N/A	ENSP00000253788.5	P61353
	RPL27	ENST00000589913.6	TSL:1	c.82-207G>T		intron	N/A	ENSP00000464813.1	P61353
	RPL27	ENST00000911442.1		c.172-207G>T		intron	N/A	ENSP00000581501.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000252 AC: 1 AN: 397526 Hom.: 0 Cov.: 3 AF XY: 0.00000481 AC XY: 1 AN XY: 207696

African (AFR) AF: 0.00 AC: 0 AN: 11700

American (AMR) AF: 0.00 AC: 0 AN: 15454

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12558

East Asian (EAS) AF: 0.00 AC: 0 AN: 28884

South Asian (SAS) AF: 0.0000276 AC: 1 AN: 36212

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1756

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 240974

Other (OTH) AF: 0.00 AC: 0 AN: 23360

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.24
PhyloP100		-0.063

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: rs691711; hg19: chr17-41151743;