ENST00000466297.1:n.55C>T

Variant names:

• chr17-4705163-G-A
• rs9895782
• ENST00000466297.1:n.55C>T

Variant summary

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

The ENST00000466297.1(ENSG00000213939):​n.55C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0432 in 737,510 control chromosomes in the GnomAD database, including 893 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 0.041 (166 hom., cov: 33)
  • Exomes 𝑓: 0.044 (727 hom.)
• Consequence: ENSG00000213939 ENST00000466297.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.42
• Publications: 1 publications found

Genes affected

ENSG00000213939 (HGNC:):

PELP1-DT (HGNC:55614): (PELP1 divergent transcript)

RPS12P29 (HGNC:36206):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466297.1. 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
	PELP1-DT	NR_103482.1		n.142-36G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000213939	ENST00000466297.1	TSL:6	n.55C>T		non_coding_transcript_exon	Exon 1 of 1
	PELP1-DT	ENST00000810537.1		n.220G>A		non_coding_transcript_exon	Exon 2 of 2
	PELP1-DT	ENST00000497885.2	TSL:2	n.262-36G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0411 AC: 6259 AN: 152198 Hom.: 167 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0642

GnomAD4 exome AF: 0.0438 AC: 25607 AN: 585194 Hom.: 727 Cov.: 6 AF XY: 0.0441 AC XY: 13922 AN XY: 315338

African (AFR) AF: 0.0281 AC: 463 AN: 16494

American (AMR) AF: 0.0345 AC: 1296 AN: 37610

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 1798 AN: 17622

East Asian (EAS) AF: 0.000477 AC: 17 AN: 35608

South Asian (SAS) AF: 0.0456 AC: 2835 AN: 62204

European-Finnish (FIN) AF: 0.0348 AC: 1369 AN: 39288

Middle Eastern (MID) AF: 0.131 AC: 405 AN: 3080

European-Non Finnish (NFE) AF: 0.0461 AC: 15773 AN: 342214

Other (OTH) AF: 0.0531 AC: 1651 AN: 31074

GnomAD4 genome AF: 0.0411 AC: 6257 AN: 152316 Hom.: 166 Cov.: 33 AF XY: 0.0418 AC XY: 3115 AN XY: 74486

African (AFR) AF: 0.0264 AC: 1096 AN: 41570

American (AMR) AF: 0.0576 AC: 882 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0424 AC: 205 AN: 4830

European-Finnish (FIN) AF: 0.0404 AC: 429 AN: 10618

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0452 AC: 3073 AN: 68024

Other (OTH) AF: 0.0636 AC: 134 AN: 2108

Alfa AF: 0.0505 Hom.: 287

Bravo AF: 0.0428

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		6.4

Splicing

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

Other links and lift over

dbSNP: rs9895782; hg19: chr17-4608458;