ENST00000400348.3:n.87T>C

Variant summary

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

The ENST00000400348.3(CTAGE12P):​n.87T>C 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 0.624 in 534,080 control chromosomes in the GnomAD database, including 105,138 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 0.64 ( 31384 hom., cov: 34)
Exomes 𝑓: 0.62 ( 73754 hom. )

Consequence

CTAGE12P
ENST00000400348.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.338

Publications

7 publications found
Variant links:
Genes affected
CTAGE12P (HGNC:37297): (CTAGE family member 12, pseudogene)

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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CTAGE12P n.27610659A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTAGE12PENST00000400348.3 linkn.87T>C non_coding_transcript_exon_variant Exon 1 of 1 6
ENSG00000307594ENST00000827310.1 linkn.697-24273T>C intron_variant Intron 3 of 3
ENSG00000307594ENST00000827311.1 linkn.389-24273T>C intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.639
AC:
97160
AN:
152036
Hom.:
31372
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.658
Gnomad AMI
AF:
0.759
Gnomad AMR
AF:
0.556
Gnomad ASJ
AF:
0.564
Gnomad EAS
AF:
0.769
Gnomad SAS
AF:
0.575
Gnomad FIN
AF:
0.623
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.646
Gnomad OTH
AF:
0.645
GnomAD4 exome
AF:
0.618
AC:
235979
AN:
381926
Hom.:
73754
Cov.:
2
AF XY:
0.616
AC XY:
133291
AN XY:
216286
show subpopulations
African (AFR)
AF:
0.661
AC:
6821
AN:
10318
American (AMR)
AF:
0.503
AC:
16313
AN:
32418
Ashkenazi Jewish (ASJ)
AF:
0.566
AC:
6230
AN:
11008
East Asian (EAS)
AF:
0.762
AC:
11757
AN:
15438
South Asian (SAS)
AF:
0.572
AC:
35894
AN:
62708
European-Finnish (FIN)
AF:
0.625
AC:
19399
AN:
31060
Middle Eastern (MID)
AF:
0.611
AC:
1697
AN:
2778
European-Non Finnish (NFE)
AF:
0.638
AC:
126792
AN:
198674
Other (OTH)
AF:
0.632
AC:
11076
AN:
17524
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
4356
8712
13067
17423
21779
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
866
1732
2598
3464
4330
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.639
AC:
97204
AN:
152154
Hom.:
31384
Cov.:
34
AF XY:
0.635
AC XY:
47262
AN XY:
74370
show subpopulations
African (AFR)
AF:
0.658
AC:
27315
AN:
41512
American (AMR)
AF:
0.555
AC:
8485
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.564
AC:
1957
AN:
3472
East Asian (EAS)
AF:
0.769
AC:
3981
AN:
5174
South Asian (SAS)
AF:
0.574
AC:
2767
AN:
4824
European-Finnish (FIN)
AF:
0.623
AC:
6584
AN:
10568
Middle Eastern (MID)
AF:
0.605
AC:
178
AN:
294
European-Non Finnish (NFE)
AF:
0.646
AC:
43893
AN:
67998
Other (OTH)
AF:
0.641
AC:
1352
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1808
3617
5425
7234
9042
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
788
1576
2364
3152
3940
<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:
0.636
Hom.:
95348
Bravo
AF:
0.636
Asia WGS
AF:
0.661
AC:
2295
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
3.3
DANN
Benign
0.42
PhyloP100
0.34

Splicing

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

Publications

Other links and lift over

dbSNP: rs2889829; hg19: chr9-27610657; API