ENST00000801024.1:n.176G>T

Variant names:

• chr6-170584930-G-T
• rs734249
• ENST00000801024.1:n.176G>T

Variant summary

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

The ENST00000801024.1(ENSG00000304206):​n.176G>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 0.472 in 152,070 control chromosomes in the GnomAD database, including 17,690 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 0.47 (17690 hom., cov: 33)
• Consequence: ENSG00000304206 ENST00000801024.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 3 publications found

Genes affected

ENSG00000304206 (HGNC:):

PDCD2 (HGNC:8762): (programmed cell death 2) This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801024.1. 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
	ENSG00000304206	ENST00000801024.1		n.176G>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000304206	ENST00000801025.1		n.158G>T		non_coding_transcript_exon	Exon 1 of 2
	PDCD2	ENST00000544336.5	TSL:1	n.-349C>A		upstream_gene	N/A	ENSP00000444066.1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71718 AN: 151952 Hom.: 17651 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.450

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.472 AC: 71801 AN: 152070 Hom.: 17690 Cov.: 33 AF XY: 0.473 AC XY: 35136 AN XY: 74334

African (AFR) AF: 0.584 AC: 24230 AN: 41496

American (AMR) AF: 0.412 AC: 6302 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3468

East Asian (EAS) AF: 0.783 AC: 4035 AN: 5150

South Asian (SAS) AF: 0.378 AC: 1820 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4781 AN: 10572

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27900 AN: 67962

Other (OTH) AF: 0.453 AC: 955 AN: 2108

Alfa AF: 0.377 Hom.: 1626

Bravo AF: 0.481

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.38
PhyloP100		-0.93
PromoterAI		0.0021	Neutral

Splicing

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

Other links and lift over

dbSNP: rs734249; hg19: chr6-170894018;