21-39659683-C-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.114

Publications

9 publications found
Variant links:
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
B3GALT5NM_001356336.2 linkc.-160-70C>T intron_variant Intron 2 of 3 ENST00000684187.2 NP_001343265.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
B3GALT5ENST00000684187.2 linkc.-160-70C>T intron_variant Intron 2 of 3 NM_001356336.2 ENSP00000506797.1 Q9Y2C3

Frequencies

GnomAD3 genomes
AF:
0.347
AC:
52570
AN:
151400
Hom.:
10961
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.129
Gnomad AMI
AF:
0.538
Gnomad AMR
AF:
0.374
Gnomad ASJ
AF:
0.520
Gnomad EAS
AF:
0.0760
Gnomad SAS
AF:
0.426
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.510
Gnomad NFE
AF:
0.458
Gnomad OTH
AF:
0.385
GnomAD4 exome
AF:
0.445
AC:
325909
AN:
733004
Hom.:
74090
AF XY:
0.446
AC XY:
152240
AN XY:
341268
show subpopulations
African (AFR)
AF:
0.0976
AC:
1344
AN:
13766
American (AMR)
AF:
0.334
AC:
287
AN:
860
Ashkenazi Jewish (ASJ)
AF:
0.520
AC:
2371
AN:
4556
East Asian (EAS)
AF:
0.0769
AC:
244
AN:
3172
South Asian (SAS)
AF:
0.434
AC:
6248
AN:
14408
European-Finnish (FIN)
AF:
0.400
AC:
100
AN:
250
Middle Eastern (MID)
AF:
0.483
AC:
701
AN:
1452
European-Non Finnish (NFE)
AF:
0.454
AC:
304553
AN:
670632
Other (OTH)
AF:
0.421
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

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
12400
24800
37200
49600
62000
<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:
0.347
AC:
52571
AN:
151468
Hom.:
10961
Cov.:
31
AF XY:
0.351
AC XY:
25941
AN XY:
73948
show subpopulations
African (AFR)
AF:
0.129
AC:
5297
AN:
41180
American (AMR)
AF:
0.374
AC:
5696
AN:
15228
Ashkenazi Jewish (ASJ)
AF:
0.520
AC:
1804
AN:
3466
East Asian (EAS)
AF:
0.0756
AC:
389
AN:
5148
South Asian (SAS)
AF:
0.426
AC:
2042
AN:
4798
European-Finnish (FIN)
AF:
0.460
AC:
4799
AN:
10426
Middle Eastern (MID)
AF:
0.524
AC:
152
AN:
290
European-Non Finnish (NFE)
AF:
0.458
AC:
31098
AN:
67924
Other (OTH)
AF:
0.383
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
518
1036
1554
2072
2590
<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:
0.425
Hom.:
26633
Bravo
AF:
0.327
Asia WGS
AF:
0.264
AC:
918
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.8
DANN
Benign
0.69
PhyloP100
0.11
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: rs2837108; hg19: chr21-41031610; API