Genetic Variant NM_001356336.2:c.-160-70C>T (chr21-39659683-C-T) – 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.-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

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]

B3GALT5 links:

ENSG00000225330 (HGNC:):

ENSG00000225330 links:

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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.

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.-160-70C>T	intron	N/A	NP_001343265.1	Q9Y2C3
B3GALT5	NM_033172.3		c.13-877C>T	intron	N/A	NP_149362.2	A0A0A0MS93
B3GALT5	NM_001278650.2		c.-160-70C>T	intron	N/A	NP_001265579.1	Q9Y2C3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
B3GALT5	ENST00000684187.2	MANE Select	c.-160-70C>T	intron	N/A	ENSP00000506797.1	Q9Y2C3
B3GALT5	ENST00000380618.5	TSL:1	c.-160-70C>T	intron	N/A	ENSP00000369992.1	Q9Y2C3
B3GALT5	ENST00000380620.8	TSL:1	c.-160-70C>T	intron	N/A	ENSP00000369994.3	Q9Y2C3

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52570

AN:

151400

Hom.:

10961

Cov.:

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

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

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.:

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

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

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.8

(source)

DANN

Benign

0.69

PhyloP100

0.11

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