rs6573295

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000491913.2. 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
	RPL17P2	ENST00000491913.2	TSL:6	n.378A>G		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6573295;

hg19: chr14-60679253;