rs78924165

Variant names:

• chr16-1964488-T-C
• rs78924165
• NM_002952.4:c.138A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-1964488-T-C
• chr16-1964488-T-G

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_002952.4(RPS2):​c.138A>G​(p.Arg46Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,607,308 control chromosomes in the GnomAD database, including 251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.021 (137 hom., cov: 34)
  • Exomes 𝑓: 0.0022 (114 hom.)
• Consequence: RPS2 NM_002952.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.560
• Publications: 2 publications found

Genes affected

RPS2 (HGNC:10404): (ribosomal protein S2) 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 S5P family of ribosomal proteins. It is located in the cytoplasm. This gene shares sequence similarity with mouse LLRep3. It is co-transcribed with the small nucleolar RNA gene U64, which is located in its third intron. 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]

SNHG9 (HGNC:33102): (small nucleolar RNA host gene 9)

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 16-1964488-T-C is Benign according to our data. Variant chr16-1964488-T-C is described in ClinVar as Benign. ClinVar VariationId is 768738.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.56 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002952.4. 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
	RPS2	NM_002952.4	MANE Select	c.138A>G	p.Arg46Arg	synonymous	Exon 2 of 7	NP_002943.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS2	ENST00000343262.9	TSL:1 MANE Select	c.138A>G	p.Arg46Arg	synonymous	Exon 2 of 7	ENSP00000341885.4	P15880
	RPS2	ENST00000527109.5	TSL:1	n.143A>G		non_coding_transcript_exon	Exon 1 of 5
	RPS2	ENST00000527826.1	TSL:1	n.318A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 3262 AN: 152084 Hom.: 136 Cov.: 34

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00681

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000176

Gnomad OTH AF: 0.0158

GnomAD2 exomes AF: 0.00507 AC: 1187 AN: 234104 AF XY: 0.00390

Gnomad AFR exome AF: 0.0790

Gnomad AMR exome AF: 0.00278

Gnomad ASJ exome AF: 0.000209

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000155

Gnomad OTH exome AF: 0.00211

GnomAD4 exome AF: 0.00216 AC: 3143 AN: 1455106 Hom.: 114 Cov.: 33 AF XY: 0.00181 AC XY: 1311 AN XY: 723754

African (AFR) AF: 0.0774 AC: 2578 AN: 33288

American (AMR) AF: 0.00358 AC: 159 AN: 44386

Ashkenazi Jewish (ASJ) AF: 0.0000385 AC: 1 AN: 25968

East Asian (EAS) AF: 0.0000253 AC: 1 AN: 39498

South Asian (SAS) AF: 0.000163 AC: 14 AN: 85924

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51576

Middle Eastern (MID) AF: 0.00328 AC: 15 AN: 4578

European-Non Finnish (NFE) AF: 0.0000784 AC: 87 AN: 1109938

Other (OTH) AF: 0.00480 AC: 288 AN: 59950

GnomAD4 genome AF: 0.0215 AC: 3271 AN: 152202 Hom.: 137 Cov.: 34 AF XY: 0.0205 AC XY: 1523 AN XY: 74416

African (AFR) AF: 0.0751 AC: 3120 AN: 41542

American (AMR) AF: 0.00680 AC: 104 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5144

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.000177 AC: 12 AN: 67988

Other (OTH) AF: 0.0156 AC: 33 AN: 2116

Alfa AF: 0.00387 Hom.: 2

Bravo AF: 0.0247

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		-0.56
PromoterAI		-0.10	Neutral
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs78924165; hg19: chr16-2014489;