rs6733349

Variant names:

• chr2-231403601-T-C
• rs6733349
• ENST00000714192.1:n.522T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000714192.1(B3GNT7):​n.522T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,100 control chromosomes in the GnomAD database, including 10,460 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 0.36 (10460 hom., cov: 32)
• Consequence: B3GNT7 ENST00000714192.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 13 publications found

Genes affected

B3GNT7 (HGNC:18811): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7) Predicted to enable UDP-glycosyltransferase activity. Predicted to be involved in poly-N-acetyllactosamine biosynthetic process. Predicted to be integral component of membrane. Predicted to be active in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GNT7	ENST00000714192.1	n.522T>C		non_coding_transcript_exon_variant	Exon 2 of 2
B3GNT7	ENST00000714191.1	c.1198-944T>C		intron_variant	Intron 2 of 3			ENSP00000519481.1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55276 AN: 151982 Hom.: 10433 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 55346 AN: 152100 Hom.: 10460 Cov.: 32 AF XY: 0.364 AC XY: 27096 AN XY: 74376

African (AFR) AF: 0.460 AC: 19053 AN: 41456

American (AMR) AF: 0.306 AC: 4673 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3472

East Asian (EAS) AF: 0.256 AC: 1325 AN: 5182

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4816

European-Finnish (FIN) AF: 0.375 AC: 3975 AN: 10588

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22376 AN: 67980

Other (OTH) AF: 0.367 AC: 775 AN: 2112

Alfa AF: 0.339 Hom.: 7159

Bravo AF: 0.361

Asia WGS AF: 0.328 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		0.097

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6733349; hg19: chr2-232268312;