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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001356336.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
B3GALT5	NM_001356336.2	MANE Select	c.*4304A>G	3_prime_UTR	Exon 4 of 4	NP_001343265.1	Q9Y2C3
B3GALT5	NM_033172.3		c.*4304A>G	3_prime_UTR	Exon 3 of 3	NP_149362.2	A0A0A0MS93
B3GALT5	NM_001278650.2		c.*4304A>G	3_prime_UTR	Exon 3 of 3	NP_001265579.1	Q9Y2C3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
B3GALT5	ENST00000684187.2	MANE Select	c.*4304A>G	3_prime_UTR	Exon 4 of 4	ENSP00000506797.1	Q9Y2C3
B3GALT5	ENST00000380620.8	TSL:1	c.*4304A>G	3_prime_UTR	Exon 5 of 5	ENSP00000369994.3	Q9Y2C3
B3GALT5	ENST00000852636.1		c.*4304A>G	3_prime_UTR	Exon 5 of 5	ENSP00000522695.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over