chr19-17807939-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_014256.4(B3GNT3):​c.132C>T​(p.Pro44=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,613,396 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0058 ( 7 hom., cov: 30)
Exomes 𝑓: 0.00062 ( 10 hom. )

Consequence

B3GNT3
NM_014256.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.16
Variant links:
Genes affected
B3GNT3 (HGNC:13528): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein and contains a signal anchor that is not cleaved. It prefers the substrates of lacto-N-tetraose and lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains and the biosynthesis of the backbone structure of dimeric sialyl Lewis a. It plays dominant roles in L-selectin ligand biosynthesis, lymphocyte homing and lymphocyte trafficking. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 19-17807939-C-T is Benign according to our data. Variant chr19-17807939-C-T is described in ClinVar as [Benign]. Clinvar id is 769962.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.16 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00578 (880/152202) while in subpopulation AFR AF= 0.0205 (851/41520). AF 95% confidence interval is 0.0194. There are 7 homozygotes in gnomad4. There are 422 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
B3GNT3NM_014256.4 linkuse as main transcriptc.132C>T p.Pro44= synonymous_variant 2/3 ENST00000318683.7 NP_055071.2
B3GNT3XM_011527626.3 linkuse as main transcriptc.132C>T p.Pro44= synonymous_variant 2/3 XP_011525928.1
B3GNT3XM_047438042.1 linkuse as main transcriptc.132C>T p.Pro44= synonymous_variant 2/3 XP_047293998.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
B3GNT3ENST00000318683.7 linkuse as main transcriptc.132C>T p.Pro44= synonymous_variant 2/31 NM_014256.4 ENSP00000321874 P1
B3GNT3ENST00000595387.1 linkuse as main transcriptc.132C>T p.Pro44= synonymous_variant 2/31 ENSP00000472638 P1
B3GNT3ENST00000599265.5 linkuse as main transcriptc.132C>T p.Pro44= synonymous_variant 2/33 ENSP00000471733
B3GNT3ENST00000600777.1 linkuse as main transcriptc.132C>T p.Pro44= synonymous_variant 2/23 ENSP00000468914

Frequencies

GnomAD3 genomes
AF:
0.00575
AC:
875
AN:
152084
Hom.:
7
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0204
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00105
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00240
GnomAD3 exomes
AF:
0.00167
AC:
414
AN:
248140
Hom.:
2
AF XY:
0.00119
AC XY:
160
AN XY:
134898
show subpopulations
Gnomad AFR exome
AF:
0.0206
Gnomad AMR exome
AF:
0.00104
Gnomad ASJ exome
AF:
0.00250
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000807
Gnomad OTH exome
AF:
0.00346
GnomAD4 exome
AF:
0.000625
AC:
913
AN:
1461194
Hom.:
10
Cov.:
30
AF XY:
0.000537
AC XY:
390
AN XY:
726916
show subpopulations
Gnomad4 AFR exome
AF:
0.0206
Gnomad4 AMR exome
AF:
0.000984
Gnomad4 ASJ exome
AF:
0.00218
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000809
Gnomad4 OTH exome
AF:
0.00113
GnomAD4 genome
AF:
0.00578
AC:
880
AN:
152202
Hom.:
7
Cov.:
30
AF XY:
0.00567
AC XY:
422
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.0205
Gnomad4 AMR
AF:
0.00105
Gnomad4 ASJ
AF:
0.00144
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00378
Hom.:
4
Bravo
AF:
0.00651
Asia WGS
AF:
0.00346
AC:
12
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
3.2
DANN
Benign
0.61

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: rs79614823; hg19: chr19-17918748; COSMIC: COSV59437415; API