GeneBe

rs12615966

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000715830.1(PANTR1):​n.151-15348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,082 control chromosomes in the GnomAD database, including 1,528 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 0.14 ( 1528 hom., cov: 32)

Consequence

PANTR1
ENST00000715830.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600

Publications

25 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PANTR1ENST00000715830.1 linkn.151-15348G>A intron_variant Intron 1 of 4
PANTR1ENST00000715831.1 linkn.245-4487G>A intron_variant Intron 1 of 4
PANTR1ENST00000733170.1 linkn.157-13010G>A intron_variant Intron 1 of 4

Frequencies

GnomAD3 genomes
AF:
0.138
AC:
20908
AN:
151964
Hom.:
1531
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.133
Gnomad AMI
AF:
0.0910
Gnomad AMR
AF:
0.176
Gnomad ASJ
AF:
0.0997
Gnomad EAS
AF:
0.0892
Gnomad SAS
AF:
0.0785
Gnomad FIN
AF:
0.192
Gnomad MID
AF:
0.210
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.148
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.137
AC:
20901
AN:
152082
Hom.:
1528
Cov.:
32
AF XY:
0.139
AC XY:
10303
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.132
AC:
5493
AN:
41468
American (AMR)
AF:
0.175
AC:
2676
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.0997
AC:
346
AN:
3472
East Asian (EAS)
AF:
0.0890
AC:
460
AN:
5166
South Asian (SAS)
AF:
0.0784
AC:
378
AN:
4822
European-Finnish (FIN)
AF:
0.192
AC:
2023
AN:
10556
Middle Eastern (MID)
AF:
0.199
AC:
58
AN:
292
European-Non Finnish (NFE)
AF:
0.133
AC:
9074
AN:
68014
Other (OTH)
AF:
0.147
AC:
310
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
920
1840
2761
3681
4601
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
230
460
690
920
1150
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.135
Hom.:
5351
Bravo
AF:
0.137
Asia WGS
AF:
0.0820
AC:
286
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
10
DANN
Benign
0.71
PhyloP100
0.0060

Splicing

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

Publications

Other links and lift over

dbSNP: rs12615966; hg19: chr2-105378957; COSMIC: COSV69871903; API