17-82977736-C-T

Position:

• chr17-82977736-C-T

Variant summary

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

The ENST00000320865.4(B3GNTL1):​c.460-11990G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,836 control chromosomes in the GnomAD database, including 19,305 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 0.50 (19305 hom., cov: 31)
• Consequence: B3GNTL1 ENST00000320865.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B3GNTL1	NM_001009905.3	c.460-11990G>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.460-11990G>A		intron_variant		1	NM_001009905.3	ENSP00000319979	P1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75970 AN: 151720 Hom.: 19294 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.501 AC: 76028 AN: 151836 Hom.: 19305 Cov.: 31 AF XY: 0.508 AC XY: 37687 AN XY: 74214

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.537

Alfa AF: 0.524 Hom.: 33361

Bravo AF: 0.492

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.60

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: rs1551628; hg19: chr17-80935612;