10-95595157-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000398190.2(RPS3AP36):​n.560C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.466 in 759,106 control chromosomes in the GnomAD database, including 88,666 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: 𝑓 0.39 (14440 hom., cov: 33)
  • Exomes 𝑓: 0.48 (74226 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

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>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59954 AN: 152018 Hom.: 14441 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.484 AC: 293583 AN: 606970 Hom.: 74226 Cov.: 4 AF XY: 0.476 AC XY: 157761 AN XY: 331606

African (AFR) AF: 0.106 AC: 1821 AN: 17246

American (AMR) AF: 0.570 AC: 24086 AN: 42234

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 7204 AN: 20562

East Asian (EAS) AF: 0.511 AC: 18351 AN: 35900

South Asian (SAS) AF: 0.373 AC: 25578 AN: 68514

European-Finnish (FIN) AF: 0.531 AC: 19725 AN: 37144

Middle Eastern (MID) AF: 0.309 AC: 1258 AN: 4074

European-Non Finnish (NFE) AF: 0.518 AC: 180648 AN: 348842

Other (OTH) AF: 0.459 AC: 14912 AN: 32454

GnomAD4 genome AF: 0.394 AC: 59953 AN: 152136 Hom.: 14440 Cov.: 33 AF XY: 0.393 AC XY: 29239 AN XY: 74362

African (AFR) AF: 0.106 AC: 4411 AN: 41528

American (AMR) AF: 0.507 AC: 7752 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1201 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2698 AN: 5184

South Asian (SAS) AF: 0.354 AC: 1706 AN: 4822

European-Finnish (FIN) AF: 0.512 AC: 5417 AN: 10572

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35473 AN: 67974

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.433 Hom.: 2116

Bravo AF: 0.386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.7
DANN	Benign	0.76
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;