ENST00000654016.1:n.43+12576A>C

Variant summary

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

The ENST00000654016.1(ENSG00000260271):​n.43+12576A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,044 control chromosomes in the GnomAD database, including 10,016 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 0.34 ( 10016 hom., cov: 32)

Consequence

ENSG00000260271
ENST00000654016.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.587

Publications

8 publications found
Variant links:
Genes affected

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 (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105377891XR_007059677.1 linkn.498+11849A>C intron_variant Intron 1 of 4
LOC105377891XR_942778.4 linkn.498+11849A>C intron_variant Intron 1 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000260271ENST00000654016.1 linkn.43+12576A>C intron_variant Intron 1 of 7
ENSG00000260271ENST00000663503.1 linkn.85+12576A>C intron_variant Intron 1 of 4
ENSG00000260271ENST00000667364.1 linkn.30+14049A>C intron_variant Intron 1 of 4

Frequencies

GnomAD3 genomes
AF:
0.341
AC:
51842
AN:
151926
Hom.:
10011
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.176
Gnomad AMI
AF:
0.421
Gnomad AMR
AF:
0.411
Gnomad ASJ
AF:
0.512
Gnomad EAS
AF:
0.135
Gnomad SAS
AF:
0.360
Gnomad FIN
AF:
0.335
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.430
Gnomad OTH
AF:
0.378
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.341
AC:
51854
AN:
152044
Hom.:
10016
Cov.:
32
AF XY:
0.337
AC XY:
25072
AN XY:
74320
show subpopulations
African (AFR)
AF:
0.176
AC:
7303
AN:
41474
American (AMR)
AF:
0.410
AC:
6269
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.512
AC:
1778
AN:
3472
East Asian (EAS)
AF:
0.135
AC:
699
AN:
5162
South Asian (SAS)
AF:
0.362
AC:
1746
AN:
4820
European-Finnish (FIN)
AF:
0.335
AC:
3539
AN:
10556
Middle Eastern (MID)
AF:
0.412
AC:
121
AN:
294
European-Non Finnish (NFE)
AF:
0.430
AC:
29224
AN:
67964
Other (OTH)
AF:
0.374
AC:
791
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1628
3257
4885
6514
8142
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
510
1020
1530
2040
2550
<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:
0.401
Hom.:
10095
Bravo
AF:
0.339
Asia WGS
AF:
0.250
AC:
871
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
6.5
DANN
Benign
0.72
PhyloP100
0.59

Splicing

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

Publications

Other links and lift over

dbSNP: rs1394220; hg19: chr6-91019304; API