rs2837076

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000380620.8(B3GALT5):​c.-524+99A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,174 control chromosomes in the GnomAD database, including 47,698 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 0.79 ( 47693 hom., cov: 32)
Exomes 𝑓: 1.0 ( 5 hom. )

Consequence

B3GALT5
ENST00000380620.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.629
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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
B3GALT5ENST00000380620.8 linkc.-524+99A>G intron_variant Intron 1 of 4 1 ENSP00000369994.3 Q9Y2C3
B3GALT5ENST00000475838.1 linkn.27+99A>G intron_variant Intron 1 of 1 5

Frequencies

GnomAD3 genomes
AF:
0.790
AC:
120174
AN:
152046
Hom.:
47663
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.779
Gnomad AMI
AF:
0.693
Gnomad AMR
AF:
0.821
Gnomad ASJ
AF:
0.766
Gnomad EAS
AF:
0.860
Gnomad SAS
AF:
0.775
Gnomad FIN
AF:
0.855
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.779
Gnomad OTH
AF:
0.786
GnomAD4 exome
AF:
1.00
AC:
10
AN:
10
Hom.:
5
AF XY:
1.00
AC XY:
8
AN XY:
8
show subpopulations
Gnomad4 AFR exome
AF:
1.00
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
1.00
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.790
AC:
120259
AN:
152164
Hom.:
47693
Cov.:
32
AF XY:
0.794
AC XY:
59055
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.779
Gnomad4 AMR
AF:
0.821
Gnomad4 ASJ
AF:
0.766
Gnomad4 EAS
AF:
0.860
Gnomad4 SAS
AF:
0.775
Gnomad4 FIN
AF:
0.855
Gnomad4 NFE
AF:
0.779
Gnomad4 OTH
AF:
0.787
Alfa
AF:
0.779
Hom.:
59475
Bravo
AF:
0.787
Asia WGS
AF:
0.826
AC:
2875
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.42
DANN
Benign
0.26

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2837076; hg19: chr21-40928536; API