chr16-87255411-T-G

Variant summary

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

The ENST00000562840.1(C16orf95):​n.110+47242A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,812 control chromosomes in the GnomAD database, including 16,476 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 0.45 ( 16476 hom., cov: 31)

Consequence

C16orf95
ENST00000562840.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.972

Publications

11 publications found
Variant links:
Genes affected
C16orf95 (HGNC:40033): (chromosome 16 open reading frame 95)

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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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
C16orf95ENST00000562840.1 linkn.110+47242A>C intron_variant Intron 1 of 4 2

Frequencies

GnomAD3 genomes
AF:
0.451
AC:
68406
AN:
151694
Hom.:
16443
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.572
Gnomad AMI
AF:
0.274
Gnomad AMR
AF:
0.380
Gnomad ASJ
AF:
0.423
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.135
Gnomad FIN
AF:
0.325
Gnomad MID
AF:
0.433
Gnomad NFE
AF:
0.466
Gnomad OTH
AF:
0.441
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.451
AC:
68490
AN:
151812
Hom.:
16476
Cov.:
31
AF XY:
0.435
AC XY:
32295
AN XY:
74208
show subpopulations
African (AFR)
AF:
0.573
AC:
23705
AN:
41386
American (AMR)
AF:
0.380
AC:
5785
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
0.423
AC:
1468
AN:
3468
East Asian (EAS)
AF:
0.105
AC:
540
AN:
5148
South Asian (SAS)
AF:
0.136
AC:
656
AN:
4806
European-Finnish (FIN)
AF:
0.325
AC:
3431
AN:
10558
Middle Eastern (MID)
AF:
0.441
AC:
128
AN:
290
European-Non Finnish (NFE)
AF:
0.465
AC:
31609
AN:
67910
Other (OTH)
AF:
0.437
AC:
919
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1851
3702
5552
7403
9254
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
600
1200
1800
2400
3000
<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:
0.451
Hom.:
65235
Bravo
AF:
0.461
Asia WGS
AF:
0.166
AC:
581
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.61
DANN
Benign
0.51
PhyloP100
-0.97

Splicing

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

Publications

Other links and lift over

dbSNP: rs3748391; hg19: chr16-87289017; API