14-60212535-T-C

Variant names:

• chr14-60212535-T-C
• rs6573295
• ENST00000491913.2:n.378A>G

Variant summary

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

The ENST00000491913.2(RPL17P2):​n.378A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0604 in 491,080 control chromosomes in the GnomAD database, including 1,532 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 0.077 (747 hom., cov: 32)
  • Exomes 𝑓: 0.053 (785 hom.)
• Consequence: RPL17P2 ENST00000491913.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.36
• Publications: 2 publications found

Genes affected

RPL17P2 (HGNC:23540): (ribosomal protein L17 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL17P2		n.60212535T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL17P2	ENST00000491913.2	n.378A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0765 AC: 11634 AN: 152156 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0660

GnomAD4 exome AF: 0.0531 AC: 17989 AN: 338806 Hom.: 785 Cov.: 0 AF XY: 0.0551 AC XY: 10757 AN XY: 195272

African (AFR) AF: 0.159 AC: 1549 AN: 9740

American (AMR) AF: 0.0470 AC: 1601 AN: 34034

Ashkenazi Jewish (ASJ) AF: 0.0826 AC: 867 AN: 10492

East Asian (EAS) AF: 0.161 AC: 2031 AN: 12616

South Asian (SAS) AF: 0.0830 AC: 5216 AN: 62834

European-Finnish (FIN) AF: 0.0176 AC: 277 AN: 15720

Middle Eastern (MID) AF: 0.0751 AC: 82 AN: 1092

European-Non Finnish (NFE) AF: 0.0314 AC: 5554 AN: 177070

Other (OTH) AF: 0.0534 AC: 812 AN: 15208

GnomAD4 genome AF: 0.0767 AC: 11681 AN: 152274 Hom.: 747 Cov.: 32 AF XY: 0.0760 AC XY: 5656 AN XY: 74460

African (AFR) AF: 0.162 AC: 6738 AN: 41524

American (AMR) AF: 0.0544 AC: 833 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 314 AN: 3472

East Asian (EAS) AF: 0.153 AC: 795 AN: 5190

South Asian (SAS) AF: 0.0872 AC: 421 AN: 4826

European-Finnish (FIN) AF: 0.0160 AC: 170 AN: 10612

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0328 AC: 2228 AN: 68024

Other (OTH) AF: 0.0672 AC: 142 AN: 2114

Alfa AF: 0.0585 Hom.: 73

Bravo AF: 0.0828

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		5.4

Splicing

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

Other links and lift over

dbSNP: rs6573295; hg19: chr14-60679253;