chr10-95595157-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS3AP36		n.95595157C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS3AP36	ENST00000398190.2	n.560C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs498055; hg19: chr10-97354914;