chr20-16586557-C-T

Variant names:

• chr20-16586557-C-T
• rs3746786
• ENST00000457002.1:n.137G>A

Variant summary

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

The ENST00000773496.1(ENSG00000273998):​n.840C>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 0.527 in 152,266 control chromosomes in the GnomAD database, including 21,657 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 0.53 (21570 hom., cov: 32)
  • Exomes 𝑓: 0.52 (87 hom.)
• Consequence: ENSG00000273998 ENST00000773496.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 3 publications found

Genes affected

RPLP0P1 (HGNC:16585): (ribosomal protein lateral stalk subunit P0 pseudogene 1)

ENSG00000273998 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773496.1. 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
	RPLP0P1	ENST00000457002.1	TSL:6	n.137G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000273998	ENST00000773496.1		n.840C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000273998	ENST00000773497.1		n.*233C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79785 AN: 151560 Hom.: 21541 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.517 AC: 304 AN: 588 Hom.: 87 Cov.: 0 AF XY: 0.494 AC XY: 178 AN XY: 360

African (AFR) AF: 0.417 AC: 5 AN: 12

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 4 AN: 6

East Asian (EAS) AF: 0.389 AC: 7 AN: 18

South Asian (SAS) AF: 0.250 AC: 2 AN: 8

European-Finnish (FIN) AF: 0.617 AC: 132 AN: 214

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.465 AC: 133 AN: 286

Other (OTH) AF: 0.447 AC: 17 AN: 38

GnomAD4 genome AF: 0.527 AC: 79868 AN: 151678 Hom.: 21570 Cov.: 32 AF XY: 0.528 AC XY: 39139 AN XY: 74134

African (AFR) AF: 0.627 AC: 25826 AN: 41162

American (AMR) AF: 0.467 AC: 7122 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1415 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3062 AN: 5156

South Asian (SAS) AF: 0.485 AC: 2334 AN: 4814

European-Finnish (FIN) AF: 0.596 AC: 6277 AN: 10540

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32312 AN: 67958

Other (OTH) AF: 0.481 AC: 1015 AN: 2112

Alfa AF: 0.464 Hom.: 8596

Bravo AF: 0.525

Asia WGS AF: 0.549 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	4.3
DANN	Benign	0.51
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs3746786; hg19: chr20-16567202;