17-83005455-C-T

Position:

• chr17-83005455-C-T

Variant summary

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

The NM_001009905.3(B3GNTL1):​c.364-245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 629,114 control chromosomes in the GnomAD database, including 95,029 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 0.52 (20977 hom., cov: 31)
  • Exomes 𝑓: 0.56 (74052 hom.)
• Consequence: B3GNTL1 NM_001009905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

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]

B3GNTL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B3GNTL1	NM_001009905.3	c.364-245G>A		intron_variant		ENST00000320865.4	NP_001009905.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GNTL1	ENST00000320865.4	c.364-245G>A		intron_variant		1	NM_001009905.3	ENSP00000319979.4

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79181 AN: 151808 Hom.: 20974 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.555 AC: 264850 AN: 477188 Hom.: 74052 AF XY: 0.558 AC XY: 140258 AN XY: 251468

Gnomad4 AFR exome AF: 0.445

Gnomad4 AMR exome AF: 0.540

Gnomad4 ASJ exome AF: 0.587

Gnomad4 EAS exome AF: 0.520

Gnomad4 SAS exome AF: 0.597

Gnomad4 FIN exome AF: 0.539

Gnomad4 NFE exome AF: 0.558

Gnomad4 OTH exome AF: 0.550

GnomAD4 genome AF: 0.521 AC: 79214 AN: 151926 Hom.: 20977 Cov.: 31 AF XY: 0.522 AC XY: 38728 AN XY: 74256

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.520

Alfa AF: 0.544 Hom.: 36946

Bravo AF: 0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
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

Other links and lift over

dbSNP: rs9901757; hg19: chr17-80963331; COSMIC: COSV57948942;