ENST00000394133.2:n.381C>T

Variant names:

• chr10-93284178-G-A
• rs2797567
• ENST00000394133.2:n.381C>T

Variant summary

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

The ENST00000394133.2(RPL17P34):​n.381C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 1,575,004 control chromosomes in the GnomAD database, including 222,031 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 0.42 (15578 hom., cov: 30)
  • Exomes 𝑓: 0.52 (206453 hom.)
• Consequence: RPL17P34 ENST00000394133.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 1 publications found

Genes affected

RPL17P34 (HGNC:36756): (ribosomal protein L17 pseudogene 34)

ENSG00000297060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL17P34		n.93284178G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL17P34	ENST00000394133.2	n.381C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000297060	ENST00000745037.1	n.170+2652G>A		intron_variant	Intron 1 of 4
ENSG00000297060	ENST00000745038.1	n.835+2652G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63659 AN: 151192 Hom.: 15576 Cov.: 30

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.522 AC: 742801 AN: 1423692 Hom.: 206453 Cov.: 36 AF XY: 0.516 AC XY: 366567 AN XY: 709950

African (AFR) AF: 0.184 AC: 6115 AN: 33216

American (AMR) AF: 0.400 AC: 17862 AN: 44626

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 14398 AN: 25992

East Asian (EAS) AF: 0.143 AC: 5597 AN: 39068

South Asian (SAS) AF: 0.283 AC: 24289 AN: 85892

European-Finnish (FIN) AF: 0.510 AC: 21117 AN: 41388

Middle Eastern (MID) AF: 0.469 AC: 1934 AN: 4122

European-Non Finnish (NFE) AF: 0.571 AC: 622136 AN: 1090038

Other (OTH) AF: 0.495 AC: 29353 AN: 59350

GnomAD4 genome AF: 0.421 AC: 63674 AN: 151312 Hom.: 15578 Cov.: 30 AF XY: 0.414 AC XY: 30550 AN XY: 73874

African (AFR) AF: 0.204 AC: 8419 AN: 41360

American (AMR) AF: 0.441 AC: 6669 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3466

East Asian (EAS) AF: 0.153 AC: 761 AN: 4962

South Asian (SAS) AF: 0.255 AC: 1223 AN: 4794

European-Finnish (FIN) AF: 0.492 AC: 5148 AN: 10468

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 37958 AN: 67830

Other (OTH) AF: 0.440 AC: 923 AN: 2100

Alfa AF: 0.475 Hom.: 2311

Bravo AF: 0.410

Asia WGS AF: 0.221 AC: 766 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.5
DANN	Benign	0.46
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2797567; hg19: chr10-95043935;