chr10-93284178-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000394133.2. 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
	RPL17P34	ENST00000394133.2	TSL:6	n.381C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000297060	ENST00000745037.1		n.170+2652G>A		intron	N/A
	ENSG00000297060	ENST00000745038.1		n.835+2652G>A		intron	N/A

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 v4.9

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;