14-49620530-T-G

Variant names:

• chr14-49620530-T-G
• rs8018849
• NM_001001.5:c.-37+32A>C

Variant summary

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

The NM_001001.5(RPL36AL):​c.-37+32A>C 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RPL36AL NM_001001.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99
• Publications: 0 publications found

Genes affected

RPL36AL (HGNC:10346): (ribosomal protein L36a like) Cytoplasmic ribosomes, 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, which shares sequence similarity with yeast ribosomal protein L44, belongs to the L44E (L36AE) family of ribosomal proteins. This gene and the human gene officially named ribosomal protein L36a (RPL36A) encode nearly identical proteins; however, they are distinct genes. Although the name of this gene has been referred to as ribosomal protein L36a (RPL36A), its official name is ribosomal protein L36a-like (RPL36AL). 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]

ENSG00000258377 (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=-0.65).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001.5. 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
	RPL36AL	NM_001001.5	MANE Select	c.-37+32A>C		intron	N/A	NP_000992.1	Q969Q0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL36AL	ENST00000298289.7	TSL:1 MANE Select	c.-37+32A>C		intron	N/A	ENSP00000346012.5	Q969Q0
	RPL36AL	ENST00000936362.1		c.-1265A>C		5_prime_UTR	Exon 1 of 2	ENSP00000606421.1
	RPL36AL	ENST00000936364.1		c.-156A>C		5_prime_UTR	Exon 1 of 2	ENSP00000606423.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 11672 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6314

African (AFR) AF: 0.00 AC: 0 AN: 256

American (AMR) AF: 0.00 AC: 0 AN: 788

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 276

East Asian (EAS) AF: 0.00 AC: 0 AN: 224

South Asian (SAS) AF: 0.00 AC: 0 AN: 1774

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 342

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 24

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 7356

Other (OTH) AF: 0.00 AC: 0 AN: 632

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.098
DANN	Benign	0.48
PhyloP100		-4.0
PromoterAI		-0.10	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8018849; hg19: chr14-50087248;