21-39659683-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001356336.2(B3GALT5):c.-160-70C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 884,472 control chromosomes in the GnomAD database, including 85,051 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 0.35 ( 10961 hom., cov: 31)
Exomes 𝑓: 0.44 ( 74090 hom. )
Consequence
B3GALT5
NM_001356336.2 intron
NM_001356336.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.114
Publications
9 publications found
Genes affected
B3GALT5 (HGNC:920): (beta-1,3-galactosyltransferase 5) This gene encodes a member of a family of membrane-bound glycoproteins. The encoded protein may synthesize type 1 Lewis antigens, which are elevated in gastrointestinal and pancreatic cancers. Alternatively spliced transcript variants using multiple alternate promoters have been observed for this gene. [provided by RefSeq, Sep 2017]
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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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GALT5 | NM_001356336.2 | c.-160-70C>T | intron_variant | Intron 2 of 3 | ENST00000684187.2 | NP_001343265.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.347 AC: 52570AN: 151400Hom.: 10961 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
52570
AN:
151400
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.445 AC: 325909AN: 733004Hom.: 74090 AF XY: 0.446 AC XY: 152240AN XY: 341268 show subpopulations
GnomAD4 exome
AF:
AC:
325909
AN:
733004
Hom.:
AF XY:
AC XY:
152240
AN XY:
341268
show subpopulations
African (AFR)
AF:
AC:
1344
AN:
13766
American (AMR)
AF:
AC:
287
AN:
860
Ashkenazi Jewish (ASJ)
AF:
AC:
2371
AN:
4556
East Asian (EAS)
AF:
AC:
244
AN:
3172
South Asian (SAS)
AF:
AC:
6248
AN:
14408
European-Finnish (FIN)
AF:
AC:
100
AN:
250
Middle Eastern (MID)
AF:
AC:
701
AN:
1452
European-Non Finnish (NFE)
AF:
AC:
304553
AN:
670632
Other (OTH)
AF:
AC:
10061
AN:
23908
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
8131
16262
24392
32523
40654
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.347 AC: 52571AN: 151468Hom.: 10961 Cov.: 31 AF XY: 0.351 AC XY: 25941AN XY: 73948 show subpopulations
GnomAD4 genome
AF:
AC:
52571
AN:
151468
Hom.:
Cov.:
31
AF XY:
AC XY:
25941
AN XY:
73948
show subpopulations
African (AFR)
AF:
AC:
5297
AN:
41180
American (AMR)
AF:
AC:
5696
AN:
15228
Ashkenazi Jewish (ASJ)
AF:
AC:
1804
AN:
3466
East Asian (EAS)
AF:
AC:
389
AN:
5148
South Asian (SAS)
AF:
AC:
2042
AN:
4798
European-Finnish (FIN)
AF:
AC:
4799
AN:
10426
Middle Eastern (MID)
AF:
AC:
152
AN:
290
European-Non Finnish (NFE)
AF:
AC:
31098
AN:
67924
Other (OTH)
AF:
AC:
804
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1555
3110
4664
6219
7774
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
918
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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