14-39672210-T-C

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.417+16402T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,886 control chromosomes in the GnomAD database, including 25,383 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 0.55 ( 25383 hom., cov: 32)

Consequence

ENSG00000258526
ENST00000650911.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680
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=-0.69).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105370461XR_001750719.2 linkn.548+16402T>C intron_variant Intron 4 of 4
LOC105370461XR_001750722.2 linkn.496+16402T>C intron_variant Intron 3 of 3
LOC105370461XR_001750723.2 linkn.567+16402T>C intron_variant Intron 4 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000258526ENST00000650911.1 linkn.417+16402T>C intron_variant Intron 3 of 5
ENSG00000258526ENST00000651829.1 linkn.1196+16402T>C intron_variant Intron 10 of 13
ENSG00000258526ENST00000652126.1 linkn.457+16402T>C intron_variant Intron 3 of 7

Frequencies

GnomAD3 genomes
AF:
0.554
AC:
84114
AN:
151764
Hom.:
25378
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.332
Gnomad AMI
AF:
0.715
Gnomad AMR
AF:
0.549
Gnomad ASJ
AF:
0.648
Gnomad EAS
AF:
0.241
Gnomad SAS
AF:
0.508
Gnomad FIN
AF:
0.640
Gnomad MID
AF:
0.649
Gnomad NFE
AF:
0.696
Gnomad OTH
AF:
0.573
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.554
AC:
84133
AN:
151886
Hom.:
25383
Cov.:
32
AF XY:
0.549
AC XY:
40766
AN XY:
74218
show subpopulations
African (AFR)
AF:
0.332
AC:
13762
AN:
41422
American (AMR)
AF:
0.549
AC:
8365
AN:
15244
Ashkenazi Jewish (ASJ)
AF:
0.648
AC:
2247
AN:
3470
East Asian (EAS)
AF:
0.241
AC:
1244
AN:
5162
South Asian (SAS)
AF:
0.509
AC:
2450
AN:
4810
European-Finnish (FIN)
AF:
0.640
AC:
6761
AN:
10556
Middle Eastern (MID)
AF:
0.650
AC:
191
AN:
294
European-Non Finnish (NFE)
AF:
0.696
AC:
47266
AN:
67910
Other (OTH)
AF:
0.567
AC:
1195
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1702
3405
5107
6810
8512
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
706
1412
2118
2824
3530
<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:
0.656
Hom.:
17163
Bravo
AF:
0.537
Asia WGS
AF:
0.351
AC:
1219
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
8.0
DANN
Benign
0.91
PhyloP100
0.068

Splicing

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

Publications

Other links and lift over

dbSNP: rs1950634; hg19: chr14-40141414; API