chr16-23754453-G-A

Variant summary

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

The ENST00000623305.1(ENSG00000279756):​n.1487C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,428 control chromosomes in the GnomAD database, including 740 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 0.075 ( 740 hom., cov: 32)
Exomes 𝑓: 0.049 ( 0 hom. )

Consequence

ENSG00000279756
ENST00000623305.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 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
ENSG00000279756ENST00000623305.1 linkn.1487C>T non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.0750
AC:
11414
AN:
152086
Hom.:
736
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.0813
Gnomad AMR
AF:
0.0568
Gnomad ASJ
AF:
0.0331
Gnomad EAS
AF:
0.000769
Gnomad SAS
AF:
0.0588
Gnomad FIN
AF:
0.00349
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0382
Gnomad OTH
AF:
0.0818
GnomAD4 exome
AF:
0.0491
AC:
11
AN:
224
Hom.:
0
Cov.:
0
AF XY:
0.0574
AC XY:
7
AN XY:
122
show subpopulations
African (AFR)
AF:
0.200
AC:
2
AN:
10
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
6
East Asian (EAS)
AF:
0.00
AC:
0
AN:
6
South Asian (SAS)
AF:
0.167
AC:
1
AN:
6
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.0407
AC:
7
AN:
172
Other (OTH)
AF:
0.0625
AC:
1
AN:
16
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
1
2
3
4
5
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:
0.0751
AC:
11430
AN:
152204
Hom.:
740
Cov.:
32
AF XY:
0.0726
AC XY:
5401
AN XY:
74434
show subpopulations
African (AFR)
AF:
0.175
AC:
7258
AN:
41488
American (AMR)
AF:
0.0567
AC:
867
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.0331
AC:
115
AN:
3472
East Asian (EAS)
AF:
0.000770
AC:
4
AN:
5192
South Asian (SAS)
AF:
0.0584
AC:
282
AN:
4826
European-Finnish (FIN)
AF:
0.00349
AC:
37
AN:
10604
Middle Eastern (MID)
AF:
0.0918
AC:
27
AN:
294
European-Non Finnish (NFE)
AF:
0.0382
AC:
2595
AN:
68010
Other (OTH)
AF:
0.0810
AC:
171
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
520
1039
1559
2078
2598
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
122
244
366
488
610
<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:
0.0497
Hom.:
912
Bravo
AF:
0.0832
Asia WGS
AF:
0.0290
AC:
102
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
3.6
DANN
Benign
0.59
PhyloP100
-0.60
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
0.98

Splicing

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

Publications

Other links and lift over

dbSNP: rs4968031; hg19: chr16-23765774; API