dbSNP rs4818065: B3GALT5:c.*4304A>G (chr21-39665796-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001356336.2(B3GALT5):c.*4304A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,222 control chromosomes in the GnomAD database, including 39,682 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 0.71 ( 39677 hom., cov: 33)

Exomes 𝑓: 0.86 ( 5 hom. )

Consequence

B3GALT5
NM_001356336.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.498

Publications

8 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]

B3GALT5 links:

ENSG00000225330 (HGNC:):

ENSG00000225330 links:

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GALT5	NM_001356336.2 link	c.*4304A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000684187.2	NP_001343265.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
B3GALT5	ENST00000684187.2 link	c.*4304A>G	3_prime_UTR_variant	Exon 4 of 4		NM_001356336.2	ENSP00000506797.1	Q9Y2C3
B3GALT5	ENST00000380620.8 link	c.*4304A>G	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000369994.3	Q9Y2C3
ENSG00000225330	ENST00000416555.1 link	n.220+35306A>G	intron_variant	Intron 1 of 2	3
B3GALT5	ENST00000682818.1 link	n.607+2180A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.709

AC:

107809

AN:

152090

Hom.:

39657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.486

Gnomad AMI

AF:

0.818

Gnomad AMR

AF:

0.763

Gnomad ASJ

AF:

0.791

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.812

Gnomad FIN

AF:

0.807

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.728

GnomAD4 exome

AF:

0.857

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.917

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.825

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.709

AC:

107858

AN:

152208

Hom.:

39677

Cov.:

AF XY:

0.711

AC XY:

52929

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.486

AC:

20167

AN:

41492

American (AMR)

AF:

0.763

AC:

11668

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.791

AC:

2746

AN:

3470

East Asian (EAS)

AF:

0.665

AC:

3439

AN:

5174

South Asian (SAS)

AF:

0.811

AC:

3915

AN:

4830

European-Finnish (FIN)

AF:

0.807

AC:

8558

AN:

10602

Middle Eastern (MID)

AF:

0.816

AC:

240

AN:

294

European-Non Finnish (NFE)

AF:

0.806

AC:

54838

AN:

68024

Other (OTH)

AF:

0.730

AC:

1541

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1480

2960

4440

5920

7400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

824

1648

2472

3296

4120

<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:

0.725

Hom.:

7986

Bravo

AF:

0.691

Asia WGS

AF:

0.750

AC:

2610

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.1

(source)

DANN

Benign

0.65

PhyloP100

0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over