rs2837076

Positions:

• chr21-39556609-A-G
• chr21-39556609-A-T

Variant summary

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

The ENST00000380620.8(B3GALT5):​c.-524+99A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,174 control chromosomes in the GnomAD database, including 47,698 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 0.79 (47693 hom., cov: 32)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: B3GALT5 ENST00000380620.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GALT5	ENST00000380620.8	c.-524+99A>G		intron_variant		1		P1
B3GALT5	ENST00000475838.1	n.27+99A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120174 AN: 152046 Hom.: 47663 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.786

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 AF XY: 1.00 AC XY: 8 AN XY: 8

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.790 AC: 120259 AN: 152164 Hom.: 47693 Cov.: 32 AF XY: 0.794 AC XY: 59055 AN XY: 74404

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.787

Alfa AF: 0.779 Hom.: 59475

Bravo AF: 0.787

Asia WGS AF: 0.826 AC: 2875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.26

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: rs2837076; hg19: chr21-40928536;