ENST00000666016.1:n.81+18767T>C

Variant summary

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

The ENST00000666016.1(ENSG00000287307):​n.81+18767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,058 control chromosomes in the GnomAD database, including 16,485 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 0.46 ( 16485 hom., cov: 33)

Consequence

ENSG00000287307
ENST00000666016.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62

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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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
ENSG00000287307ENST00000666016.1 linkn.81+18767T>C intron_variant Intron 1 of 1
ENSG00000306201ENST00000816239.1 linkn.*85A>G downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.460
AC:
69871
AN:
151938
Hom.:
16483
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.369
Gnomad AMI
AF:
0.576
Gnomad AMR
AF:
0.483
Gnomad ASJ
AF:
0.611
Gnomad EAS
AF:
0.580
Gnomad SAS
AF:
0.551
Gnomad FIN
AF:
0.452
Gnomad MID
AF:
0.592
Gnomad NFE
AF:
0.485
Gnomad OTH
AF:
0.486
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.460
AC:
69905
AN:
152058
Hom.:
16485
Cov.:
33
AF XY:
0.462
AC XY:
34365
AN XY:
74322
show subpopulations
African (AFR)
AF:
0.369
AC:
15318
AN:
41480
American (AMR)
AF:
0.482
AC:
7370
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.611
AC:
2120
AN:
3472
East Asian (EAS)
AF:
0.580
AC:
3003
AN:
5176
South Asian (SAS)
AF:
0.549
AC:
2646
AN:
4818
European-Finnish (FIN)
AF:
0.452
AC:
4774
AN:
10560
Middle Eastern (MID)
AF:
0.605
AC:
178
AN:
294
European-Non Finnish (NFE)
AF:
0.485
AC:
32940
AN:
67956
Other (OTH)
AF:
0.488
AC:
1031
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1907
3814
5720
7627
9534
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
648
1296
1944
2592
3240
<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:
0.456
Hom.:
7422
Bravo
AF:
0.459
Asia WGS
AF:
0.564
AC:
1963
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.082
DANN
Benign
0.49
PhyloP100
-1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs12603925; hg19: chr17-14988987; API