17-38850224-AAAAATAAAAT-A

Variant names:

• chr17-38850224-AAAAATAAAAT-A
• rs540966358
• NM_000978.4:c.341-20_341-11delATTTTATTTT

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_000978.4(RPL23):​c.341-20_341-11delATTTTATTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,434,222 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000056 (0 hom.)
• Consequence: RPL23 NM_000978.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.38

Genes affected

RPL23 (HGNC:10316): (ribosomal protein L23) 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 L14P family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as rpL17 because the encoded protein shares amino acid identity with ribosomal protein L17 from Saccharomyces cerevisiae; however, its official symbol is RPL23. 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

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 17-38850224-AAAAATAAAAT-A is Benign according to our data. Variant chr17-38850224-AAAAATAAAAT-A is described in ClinVar as [Likely_benign]. Clinvar id is 2031940.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAdExome4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL23	NM_000978.4	c.341-20_341-11delATTTTATTTT		intron_variant	Intron 4 of 4	ENST00000479035.7	NP_000969.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL23	ENST00000479035.7	c.341-20_341-11delATTTTATTTT		intron_variant	Intron 4 of 4	1	NM_000978.4	ENSP00000420311.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000433 AC: 1 AN: 231182 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000473

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000558 AC: 8 AN: 1434222 Hom.: 0 AF XY: 0.00000701 AC XY: 5 AN XY: 713500

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 31688

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 40110

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25298

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39280

Gnomad4 SAS exome AF: 0.0000370 AC: 3 AN: 81144

Gnomad4 FIN exome AF: 0.0000189 AC: 1 AN: 52776

Gnomad4 NFE exome AF: 0.00000363 AC: 4 AN: 1100542

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 59038

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 22, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely 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: rs540966358; hg19: chr17-37006477;