rs498055

Variant names:

• chr10-95595157-C-A
• rs498055
• ENST00000398190.2:n.560C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-95595157-C-A
• chr10-95595157-C-G
• chr10-95595157-C-T

Variant summary

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

The ENST00000398190.2(RPS3AP36):​n.560C>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0000181 in 607,320 control chromosomes in the GnomAD database, including 1 homozygotes. 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: 0.000018 (1 hom.)
• Consequence: RPS3AP36 ENST00000398190.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.65
• Publications: 10 publications found

Genes affected

RPS3AP36 (HGNC:35596): (RPS3A pseudogene 36)

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=-0.49).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000398190.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS3AP36	ENST00000398190.2	TSL:6	n.560C>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000181 AC: 11 AN: 607320 Hom.: 1 Cov.: 4 AF XY: 0.0000301 AC XY: 10 AN XY: 331808

African (AFR) AF: 0.00 AC: 0 AN: 17254

American (AMR) AF: 0.00 AC: 0 AN: 42282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20572

East Asian (EAS) AF: 0.00 AC: 0 AN: 35904

South Asian (SAS) AF: 0.000146 AC: 10 AN: 68562

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37166

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4078

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 349032

Other (OTH) AF: 0.0000308 AC: 1 AN: 32470

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	5.7
DANN	Benign	0.79
PhyloP100		3.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs498055;

hg19: chr10-97354914;