rs1179448621

Variant names:

• chr5-172968481-G-C
• rs1179448621
• NM_016093.4:c.191G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-172968481-G-C
• chr5-172968481-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_016093.4(RPL26L1):​c.191G>C​(p.Gly64Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: RPL26L1 NM_016093.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.57

Genes affected

RPL26L1 (HGNC:17050): (ribosomal protein L26 like 1) This gene encodes a protein that shares high sequence similarity with ribosomal protein L26. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.902

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL26L1	NM_016093.4	c.191G>C	p.Gly64Ala	missense_variant	Exon 3 of 4	ENST00000265100.6	NP_057177.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL26L1	ENST00000265100.6	c.191G>C	p.Gly64Ala	missense_variant	Exon 3 of 4	1	NM_016093.4	ENSP00000265100.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.57	D;D;D;D;T
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.90
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	.;.;.;D;D
M_CAP	Benign	0.034	D
MetaRNN	Pathogenic	0.90	D;D;D;D;D
MetaSVM	Uncertain	0.55	D
MutationAssessor	Pathogenic	4.1	H;H;H;H;.
PrimateAI	Uncertain	0.61	T
PROVEAN	Uncertain	-4.2	D;D;D;D;D
REVEL	Uncertain	0.56
Sift	Uncertain	0.0080	D;D;D;D;D
Sift4G	Uncertain	0.050	T;T;T;T;T
Polyphen		0.98	D;D;D;D;.
Vest4		0.76
MutPred		0.76		Loss of stability (P = 0.0541);Loss of stability (P = 0.0541);Loss of stability (P = 0.0541);Loss of stability (P = 0.0541);Loss of stability (P = 0.0541);
MVP		0.78
MPC		1.4
ClinPred		1.0	D
GERP RS		4.6
Varity_R		0.57
gMVP		0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs1179448621; hg19: chr5-172395484;