GeneBe

16-84121084-C-T

Variant names:

Variant summary

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

The ENST00000563242.2(ENSG00000260410):​n.952-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,898 control chromosomes in the GnomAD database, including 18,508 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 0.49 ( 18503 hom., cov: 32)
Exomes 𝑓: 0.50 ( 5 hom. )

Consequence

ENSG00000260410
ENST00000563242.2 splice_region, intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.281

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=-0.73).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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
ENSG00000260410ENST00000563242.2 linkn.952-6C>T splice_region_variant, intron_variant Intron 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.492
AC:
74681
AN:
151732
Hom.:
18481
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.491
Gnomad AMI
AF:
0.566
Gnomad AMR
AF:
0.526
Gnomad ASJ
AF:
0.532
Gnomad EAS
AF:
0.657
Gnomad SAS
AF:
0.427
Gnomad FIN
AF:
0.502
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.472
Gnomad OTH
AF:
0.514
GnomAD4 exome
AF:
0.500
AC:
24
AN:
48
Hom.:
5
Cov.:
0
AF XY:
0.533
AC XY:
16
AN XY:
30
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
4
American (AMR)
AF:
0.500
AC:
1
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.625
AC:
10
AN:
16
Middle Eastern (MID)
AF:
0.500
AC:
1
AN:
2
European-Non Finnish (NFE)
AF:
0.500
AC:
11
AN:
22
Other (OTH)
AF:
0.500
AC:
1
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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:
0.492
AC:
74750
AN:
151850
Hom.:
18503
Cov.:
32
AF XY:
0.494
AC XY:
36632
AN XY:
74186
show subpopulations
African (AFR)
AF:
0.490
AC:
20306
AN:
41400
American (AMR)
AF:
0.527
AC:
8034
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
0.532
AC:
1828
AN:
3436
East Asian (EAS)
AF:
0.658
AC:
3389
AN:
5152
South Asian (SAS)
AF:
0.428
AC:
2061
AN:
4816
European-Finnish (FIN)
AF:
0.502
AC:
5294
AN:
10536
Middle Eastern (MID)
AF:
0.538
AC:
157
AN:
292
European-Non Finnish (NFE)
AF:
0.472
AC:
32088
AN:
67948
Other (OTH)
AF:
0.511
AC:
1078
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1942
3884
5827
7769
9711
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
672
1344
2016
2688
3360
<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:
0.480
Hom.:
47996
Bravo
AF:
0.497
Asia WGS
AF:
0.516
AC:
1790
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
0.58
DANN
Benign
0.65
PhyloP100
0.28

Splicing

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

Publications

Other links and lift over

dbSNP: rs8045610; hg19: chr16-84154689; COSMIC: COSV54741172; API