ENST00000669335.1:n.4095-24542T>A

Variant names:

• chr2-104681545-A-T
• rs1517853
• ENST00000669335.1:n.4095-24542T>A

Variant summary

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

The ENST00000669335.1(PANTR1):​n.4095-24542T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,152 control chromosomes in the GnomAD database, including 34,250 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 0.63 (34250 hom., cov: 32)
• Consequence: PANTR1 ENST00000669335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 1 publications found

Genes affected

PANTR1 (HGNC:49513): (POU3F3 adjacent non-coding transcript 1) Predicted to act upstream of or within regulation of gene expression. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230690 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373526	NR_188087.1	n.1124-3175A>T		intron_variant	Intron 6 of 6
LOC105373526	NR_188088.1	n.1168+1065A>T		intron_variant	Intron 7 of 8
LOC105373526	NR_188089.1	n.988+1065A>T		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANTR1	ENST00000669335.1	n.4095-24542T>A		intron_variant	Intron 1 of 1
PANTR1	ENST00000715830.1	n.1419-24542T>A		intron_variant	Intron 4 of 4
PANTR1	ENST00000733170.1	n.1715-24542T>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96391 AN: 152034 Hom.: 34250 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.634 AC: 96389 AN: 152152 Hom.: 34250 Cov.: 32 AF XY: 0.635 AC XY: 47241 AN XY: 74378

African (AFR) AF: 0.293 AC: 12160 AN: 41502

American (AMR) AF: 0.652 AC: 9978 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2492 AN: 3472

East Asian (EAS) AF: 0.573 AC: 2951 AN: 5152

South Asian (SAS) AF: 0.701 AC: 3373 AN: 4810

European-Finnish (FIN) AF: 0.834 AC: 8835 AN: 10598

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54105 AN: 68006

Other (OTH) AF: 0.672 AC: 1421 AN: 2114

Alfa AF: 0.706 Hom.: 5047

Bravo AF: 0.603

Asia WGS AF: 0.614 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.68
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1517853; hg19: chr2-105298003;