rs13030174

Variant names:

• chr2-231406573-A-C
• rs13030174
• ENST00000714192.1:n.3494A>C

Variant summary

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

The ENST00000714192.1(B3GNT7):​n.3494A>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 0.213 in 152,098 control chromosomes in the GnomAD database, including 3,822 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 0.21 (3822 hom., cov: 32)
• Consequence: B3GNT7 ENST00000714192.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 29 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 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.3494A>C		non_coding_transcript_exon_variant	Exon 2 of 2
B3GNT7	ENST00000714191.1	c.*325A>C		3_prime_UTR_variant	Exon 4 of 4			ENSP00000519481.1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32369 AN: 151980 Hom.: 3821 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.213 AC: 32381 AN: 152098 Hom.: 3822 Cov.: 32 AF XY: 0.219 AC XY: 16257 AN XY: 74346

African (AFR) AF: 0.104 AC: 4309 AN: 41516

American (AMR) AF: 0.219 AC: 3343 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1316 AN: 5174

South Asian (SAS) AF: 0.275 AC: 1325 AN: 4818

European-Finnish (FIN) AF: 0.333 AC: 3508 AN: 10548

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16752 AN: 67982

Other (OTH) AF: 0.237 AC: 500 AN: 2110

Alfa AF: 0.235 Hom.: 13484

Bravo AF: 0.198

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.23
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs13030174; hg19: chr2-232271284;