rs12603456

chr17-82981284-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009905.3(B3GNTL1):c.460-15538T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,136 control chromosomes in the GnomAD database, including 5,769 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 0.27 (5769 hom., cov: 33)
  • Exomes 𝑓: 0.22 (0 hom.)
• Consequence: B3GNTL1 NM_001009905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

B3GNTL1 (HGNC:21727): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1) Predicted to enable glycosyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GNTL1	NM_001009905.3	c.460-15538T>A		intron_variant		ENST00000320865.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GNTL1	ENST00000320865.4	c.460-15538T>A		intron_variant		1	NM_001009905.3	P1
	ENST00000573207.1	n.105-175A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40929 AN: 151982 Hom.: 5768 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.222 AC: 8 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 8 AN XY: 32

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.269 AC: 40952 AN: 152100 Hom.: 5769 Cov.: 33 AF XY: 0.264 AC XY: 19606 AN XY: 74378

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.253

Alfa AF: 0.261 Hom.: 666

Bravo AF: 0.278

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.7
Dann	Benign	0.69

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: rs12603456; hg19: chr17-80939160;