rs2239385

chr21-39655820-G-A

Variant summary

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

The NM_001356336.2(B3GALT5):c.-160-3933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,974 control chromosomes in the GnomAD database, including 39,513 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 0.72 (39513 hom., cov: 31)
• Consequence: B3GALT5 NM_001356336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

Genes affected

B3GALT5 (HGNC:920): (beta-1,3-galactosyltransferase 5) This gene encodes a member of a family of membrane-bound glycoproteins. The encoded protein may synthesize type 1 Lewis antigens, which are elevated in gastrointestinal and pancreatic cancers. Alternatively spliced transcript variants using multiple alternate promoters have been observed for this gene. [provided by RefSeq, Sep 2017]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GALT5	NM_001356336.2	c.-160-3933G>A		intron_variant		ENST00000684187.2
B3GALT5	NM_001278650.2	c.-160-3933G>A		intron_variant
B3GALT5	NM_001356338.2	c.-160-3933G>A		intron_variant
B3GALT5	NM_001356339.2	c.-160-3933G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GALT5	ENST00000684187.2	c.-160-3933G>A		intron_variant			NM_001356336.2	P1
	ENST00000416555.1	n.220+25330G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108996 AN: 151856 Hom.: 39485 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.718 AC: 109078 AN: 151974 Hom.: 39513 Cov.: 31 AF XY: 0.717 AC XY: 53282 AN XY: 74270

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.728

Alfa AF: 0.734 Hom.: 55767

Bravo AF: 0.708

Asia WGS AF: 0.682 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.40
Dann	Benign	0.48

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: rs2239385; hg19: chr21-41027747;