GeneBe

rs6542736

Variant names:

Variant summary

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

The ENST00000419650.1(GACAT1):​n.246-11434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,938 control chromosomes in the GnomAD database, including 8,458 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 0.32 ( 8458 hom., cov: 32)

Consequence

GACAT1
ENST00000419650.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.247

Publications

2 publications found
Variant links:
Genes affected
GACAT1 (HGNC:48336): (gastric cancer associated transcript 1)

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=-0.93).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GACAT1NR_126369.1 linkn.279-11434G>A intron_variant Intron 2 of 3
GACAT1NR_126370.1 linkn.279-11434G>A intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GACAT1ENST00000419650.1 linkn.246-11434G>A intron_variant Intron 2 of 3 4
GACAT1ENST00000441383.5 linkn.279-11434G>A intron_variant Intron 2 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.324
AC:
49248
AN:
151820
Hom.:
8447
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.564
Gnomad AMR
AF:
0.348
Gnomad ASJ
AF:
0.433
Gnomad EAS
AF:
0.330
Gnomad SAS
AF:
0.478
Gnomad FIN
AF:
0.329
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.370
Gnomad OTH
AF:
0.337
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.324
AC:
49274
AN:
151938
Hom.:
8458
Cov.:
32
AF XY:
0.326
AC XY:
24194
AN XY:
74250
show subpopulations
African (AFR)
AF:
0.205
AC:
8475
AN:
41438
American (AMR)
AF:
0.348
AC:
5312
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.433
AC:
1503
AN:
3472
East Asian (EAS)
AF:
0.331
AC:
1701
AN:
5138
South Asian (SAS)
AF:
0.478
AC:
2299
AN:
4808
European-Finnish (FIN)
AF:
0.329
AC:
3478
AN:
10556
Middle Eastern (MID)
AF:
0.456
AC:
134
AN:
294
European-Non Finnish (NFE)
AF:
0.370
AC:
25138
AN:
67956
Other (OTH)
AF:
0.344
AC:
724
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1660
3320
4981
6641
8301
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
498
996
1494
1992
2490
<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:
0.359
Hom.:
43076
Bravo
AF:
0.318
Asia WGS
AF:
0.439
AC:
1526
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.9
DANN
Benign
0.38
PhyloP100
0.25

Splicing

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

Publications

Other links and lift over

dbSNP: rs6542736; hg19: chr2-108415702; API