GeneBe

16-77906637-A-G

Variant names:

Variant summary

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

The NM_020927.3(VAT1L):​c.1077+21835A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,114 control chromosomes in the GnomAD database, including 3,729 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 0.22 ( 3729 hom., cov: 32)

Consequence

VAT1L
NM_020927.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.724

Publications

3 publications found
Variant links:
Genes affected
VAT1L (HGNC:29315): (vesicle amine transport 1 like) Predicted to enable oxidoreductase activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VAT1LNM_020927.3 linkc.1077+21835A>G intron_variant Intron 7 of 8 ENST00000302536.3 NP_065978.1 Q9HCJ6A8K288

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VAT1LENST00000302536.3 linkc.1077+21835A>G intron_variant Intron 7 of 8 1 NM_020927.3 ENSP00000303129.2 Q9HCJ6

Frequencies

GnomAD3 genomes
AF:
0.218
AC:
33199
AN:
151994
Hom.:
3727
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.204
Gnomad AMI
AF:
0.179
Gnomad AMR
AF:
0.153
Gnomad ASJ
AF:
0.242
Gnomad EAS
AF:
0.148
Gnomad SAS
AF:
0.260
Gnomad FIN
AF:
0.239
Gnomad MID
AF:
0.197
Gnomad NFE
AF:
0.241
Gnomad OTH
AF:
0.213
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.218
AC:
33224
AN:
152114
Hom.:
3729
Cov.:
32
AF XY:
0.217
AC XY:
16169
AN XY:
74362
show subpopulations
African (AFR)
AF:
0.204
AC:
8471
AN:
41496
American (AMR)
AF:
0.153
AC:
2340
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.242
AC:
840
AN:
3466
East Asian (EAS)
AF:
0.149
AC:
772
AN:
5180
South Asian (SAS)
AF:
0.259
AC:
1247
AN:
4820
European-Finnish (FIN)
AF:
0.239
AC:
2525
AN:
10568
Middle Eastern (MID)
AF:
0.195
AC:
57
AN:
292
European-Non Finnish (NFE)
AF:
0.241
AC:
16364
AN:
67984
Other (OTH)
AF:
0.211
AC:
445
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1347
2694
4041
5388
6735
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
372
744
1116
1488
1860
<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:
0.235
Hom.:
2262
Bravo
AF:
0.206
Asia WGS
AF:
0.187
AC:
650
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.74
DANN
Benign
0.35
PhyloP100
-0.72
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs10514431; hg19: chr16-77940534; API