rs1251704664

Variant names:

• chr19-17808102-C-G
• rs1251704664
• NM_014256.4:c.295C>G

Your query was ambiguous. Multiple possible variants found:

• chr19-17808102-C-G
• chr19-17808102-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014256.4(B3GNT3):​c.295C>G​(p.Pro99Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: B3GNT3 NM_014256.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1624974).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GNT3	NM_014256.4	c.295C>G	p.Pro99Ala	missense_variant	Exon 2 of 3	ENST00000318683.7	NP_055071.2
B3GNT3	XM_011527626.3	c.295C>G	p.Pro99Ala	missense_variant	Exon 2 of 3		XP_011525928.1
B3GNT3	XM_047438042.1	c.295C>G	p.Pro99Ala	missense_variant	Exon 2 of 3		XP_047293998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GNT3	ENST00000318683.7	c.295C>G	p.Pro99Ala	missense_variant	Exon 2 of 3	1	NM_014256.4	ENSP00000321874.5
B3GNT3	ENST00000595387.1	c.295C>G	p.Pro99Ala	missense_variant	Exon 2 of 3	1		ENSP00000472638.1
B3GNT3	ENST00000599265.5	c.295C>G	p.Pro99Ala	missense_variant	Exon 2 of 3	3		ENSP00000471733.1
B3GNT3	ENST00000600777.1	c.295C>G	p.Pro99Ala	missense_variant	Exon 2 of 2	3		ENSP00000468914.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.6
DANN	Benign	0.87
DEOGEN2	Benign	0.019	T;T;T;T
Eigen	Benign	-0.73
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.54	T;.;T;T
M_CAP	Benign	0.026	D
MetaRNN	Benign	0.16	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.9	.;L;.;L
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.89	.;N;.;.
REVEL	Benign	0.069
Sift	Uncertain	0.0080	.;D;.;.
Sift4G	Uncertain	0.039	D;T;D;T
Polyphen		0.82	.;P;.;P
Vest4		0.11, 0.11
MutPred		0.52		Loss of ubiquitination at K102 (P = 0.0962);Loss of ubiquitination at K102 (P = 0.0962);Loss of ubiquitination at K102 (P = 0.0962);Loss of ubiquitination at K102 (P = 0.0962);
MVP		0.31
MPC		0.68
ClinPred		0.32	T
GERP RS		0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.059
gMVP		0.74

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

Other links and lift over

dbSNP: rs1251704664; hg19: chr19-17918911;