ENST00000676649.1:n.447-18054T>C

Variant summary

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

The ENST00000676649.1(ENSG00000288659):​n.447-18054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,930 control chromosomes in the GnomAD database, including 29,571 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 0.61 ( 29571 hom., cov: 31)

Consequence

ENSG00000288659
ENST00000676649.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.593

Publications

2 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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC101927145XR_938809.3 linkn.372-18054T>C intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000288659ENST00000676649.1 linkn.447-18054T>C intron_variant Intron 3 of 3
ENSG00000288659ENST00000687436.3 linkn.416-18054T>C intron_variant Intron 2 of 2
ENSG00000288659ENST00000702460.2 linkn.287-12372T>C intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.613
AC:
93055
AN:
151812
Hom.:
29560
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.454
Gnomad AMI
AF:
0.707
Gnomad AMR
AF:
0.633
Gnomad ASJ
AF:
0.736
Gnomad EAS
AF:
0.395
Gnomad SAS
AF:
0.680
Gnomad FIN
AF:
0.671
Gnomad MID
AF:
0.652
Gnomad NFE
AF:
0.700
Gnomad OTH
AF:
0.607
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.613
AC:
93094
AN:
151930
Hom.:
29571
Cov.:
31
AF XY:
0.613
AC XY:
45530
AN XY:
74280
show subpopulations
African (AFR)
AF:
0.454
AC:
18809
AN:
41426
American (AMR)
AF:
0.633
AC:
9668
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.736
AC:
2554
AN:
3468
East Asian (EAS)
AF:
0.395
AC:
2032
AN:
5148
South Asian (SAS)
AF:
0.680
AC:
3277
AN:
4816
European-Finnish (FIN)
AF:
0.671
AC:
7070
AN:
10542
Middle Eastern (MID)
AF:
0.650
AC:
191
AN:
294
European-Non Finnish (NFE)
AF:
0.700
AC:
47586
AN:
67946
Other (OTH)
AF:
0.600
AC:
1265
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1764
3528
5293
7057
8821
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
772
1544
2316
3088
3860
<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:
0.671
Hom.:
127476
Bravo
AF:
0.600
Asia WGS
AF:
0.508
AC:
1767
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.4
DANN
Benign
0.46
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: rs1563796; hg19: chr4-63067995; API