rs199719364

Variant names:

• chr6-42884659-C-A
• rs199719364
• NM_001366481.3:c.358C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-42884659-C-A
• chr6-42884659-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001366481.3(RPL7L1):​c.358C>A​(p.Arg120Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RPL7L1 NM_001366481.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21

Genes affected

RPL7L1 (HGNC:21370): (ribosomal protein L7 like 1) Enables RNA binding activity. Predicted to be involved in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to act upstream of or within blastocyst formation. Predicted to be located in nucleolus. Predicted to be part of cytosolic large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL7L1	NM_001366481.3	c.358C>A	p.Arg120Ser	missense_variant	Exon 4 of 6	ENST00000493763.7	NP_001353410.1
RPL7L1	NM_198486.5	c.358C>A	p.Arg120Ser	missense_variant	Exon 4 of 7		NP_940888.3
RPL7L1	NR_134562.3	n.769C>A		non_coding_transcript_exon_variant	Exon 4 of 7
RPL7L1	NR_134563.3	n.547C>A		non_coding_transcript_exon_variant	Exon 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL7L1	ENST00000493763.7	c.358C>A	p.Arg120Ser	missense_variant	Exon 4 of 6	1	NM_001366481.3	ENSP00000418221.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.17
CADD	Pathogenic	26
DANN	Uncertain	0.99
Eigen	Uncertain	0.21
Eigen_PC	Uncertain	0.25
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.29	.;T
M_CAP	Benign	0.032	D
MetaRNN	Uncertain	0.45	T;T
MetaSVM	Uncertain	-0.26	T
PrimateAI	Uncertain	0.54	T
REVEL	Uncertain	0.33
MVP		0.67
MPC		0.60
ClinPred		0.99	D
GERP RS		4.3
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs199719364; hg19: chr6-42852397;