rs2239385

Variant names:

• chr21-39655820-G-A
• rs2239385
• NM_001356336.2:c.-160-3933G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000225330 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
B3GALT5	NM_001356336.2	c.-160-3933G>A		intron_variant	Intron 2 of 3	ENST00000684187.2	NP_001343265.1
B3GALT5	NM_001278650.2	c.-160-3933G>A		intron_variant	Intron 1 of 2		NP_001265579.1
B3GALT5	NM_001356338.2	c.-160-3933G>A		intron_variant	Intron 2 of 3		NP_001343267.1
B3GALT5	NM_001356339.2	c.-160-3933G>A		intron_variant	Intron 1 of 2		NP_001343268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GALT5	ENST00000684187.2	c.-160-3933G>A		intron_variant	Intron 2 of 3		NM_001356336.2	ENSP00000506797.1

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

African (AFR) AF: 0.710 AC: 29408 AN: 41444

American (AMR) AF: 0.676 AC: 10336 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2189 AN: 5132

South Asian (SAS) AF: 0.797 AC: 3828 AN: 4804

European-Finnish (FIN) AF: 0.751 AC: 7938 AN: 10568

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50566 AN: 67964

Other (OTH) AF: 0.728 AC: 1535 AN: 2108

Alfa AF: 0.731 Hom.: 76636

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
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2239385; hg19: chr21-41027747;