chr13-31215032-CTTT-C

Variant names:

• chr13-31215032-CTTT-C
• rs398022187
• NM_194318.4:c.71-7_71-5delTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_194318.4(B3GLCT):​c.71-7_71-5delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000242 in 1,248,924 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000021 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00027 (0 hom.)
• Consequence: B3GLCT NM_194318.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775

Genes affected

B3GLCT (HGNC:20207): (beta 3-glucosyltransferase) The protein encoded by this gene is a beta-1,3-glucosyltransferase that transfers glucose to O-linked fucosylglycans on thrombospondin type-1 repeats (TSRs) of several proteins. The encoded protein is a type II membrane protein. Defects in this gene are a cause of Peters-plus syndrome (PPS).[provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.71-7_71-5delTTT		splice_region_variant, intron_variant	Intron 1 of 14	ENST00000343307.5	NP_919299.3
B3GLCT	XM_006719768.4	c.14-7_14-5delTTT		splice_region_variant, intron_variant	Intron 1 of 14		XP_006719831.1
B3GLCT	XM_011534936.2	c.71-7_71-5delTTT		splice_region_variant, intron_variant	Intron 1 of 13		XP_011533238.1
B3GLCT	XM_047430111.1	c.71-7_71-5delTTT		splice_region_variant, intron_variant	Intron 1 of 11		XP_047286067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.71-18_71-16delTTT		intron_variant	Intron 1 of 14	1	NM_194318.4	ENSP00000343002.4

Frequencies

GnomAD3 genomes AF: 0.0000206 AC: 3 AN: 145966 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000681

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000224

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000634 AC: 83 AN: 130932 Hom.: 0 AF XY: 0.000623 AC XY: 44 AN XY: 70650

Gnomad AFR exome AF: 0.000529

Gnomad AMR exome AF: 0.000581

Gnomad ASJ exome AF: 0.000896

Gnomad EAS exome AF: 0.000217

Gnomad SAS exome AF: 0.000705

Gnomad FIN exome AF: 0.00152

Gnomad NFE exome AF: 0.000526

Gnomad OTH exome AF: 0.000888

GnomAD4 exome AF: 0.000271 AC: 299 AN: 1102958 Hom.: 0 AF XY: 0.000251 AC XY: 139 AN XY: 553466

Gnomad4 AFR exome AF: 0.000339

Gnomad4 AMR exome AF: 0.000553

Gnomad4 ASJ exome AF: 0.000145

Gnomad4 EAS exome AF: 0.0000311

Gnomad4 SAS exome AF: 0.000375

Gnomad4 FIN exome AF: 0.00110

Gnomad4 NFE exome AF: 0.000223

Gnomad4 OTH exome AF: 0.000345

GnomAD4 genome AF: 0.0000206 AC: 3 AN: 145966 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 70780

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000681

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000224

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00263 Hom.: 2424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs398022187; hg19: chr13-31789169;