2-3575633-C-G

Variant names:

• chr2-3575633-C-G
• rs568240834
• NM_001011.4:c.24C>G

Variant summary

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

The NM_001011.4(RPS7):​c.24C>G​(p.Ile8Met) 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: 33)
• Consequence: RPS7 NM_001011.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

RPS7 (HGNC:10440): (ribosomal protein S7) 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 40S subunit. The protein belongs to the S7E family of ribosomal proteins. It is located in the cytoplasm. 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

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
RPS7	NM_001011.4	c.24C>G	p.Ile8Met	missense_variant	Exon 2 of 7	ENST00000645674.2	NP_001002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS7	ENST00000645674.2	c.24C>G	p.Ile8Met	missense_variant	Exon 2 of 7		NM_001011.4	ENSP00000496757.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.80
BayesDel_addAF	Uncertain	0.028	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.50	T;T;T;.;T;T;.;T
Eigen	Benign	-0.15
Eigen_PC	Benign	-0.36
FATHMM_MKL	Benign	0.10	N
LIST_S2	Uncertain	0.96	.;.;.;D;.;.;D;D
M_CAP	Uncertain	0.27	D
MetaRNN	Uncertain	0.73	D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.58	T
MutationAssessor	Pathogenic	3.0	M;M;M;.;M;M;.;M
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-2.2	N;.;.;.;.;N;N;N
REVEL	Uncertain	0.37
Sift	Uncertain	0.0080	D;.;.;.;.;D;D;D
Sift4G	Uncertain	0.0070	D;.;.;.;.;D;D;D
Polyphen		0.99	D;D;D;.;D;D;D;D
Vest4		0.79
MutPred		0.77		Loss of methylation at K7 (P = 0.0321);Loss of methylation at K7 (P = 0.0321);Loss of methylation at K7 (P = 0.0321);Loss of methylation at K7 (P = 0.0321);Loss of methylation at K7 (P = 0.0321);Loss of methylation at K7 (P = 0.0321);Loss of methylation at K7 (P = 0.0321);Loss of methylation at K7 (P = 0.0321);
MVP		0.54
MPC		2.4
ClinPred		0.98	D
GERP RS		-1.3
Varity_R		0.50
gMVP		0.48

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: rs568240834; hg19: chr2-3623223;