rs2837076

Variant names:

• chr21-39556609-A-G
• rs2837076
• ENST00000380620.8:c.-524+99A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

B3GALT5-AS1 (HGNC:16424): (B3GALT5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GALT5	ENST00000380620.8	c.-524+99A>G		intron_variant	Intron 1 of 4	1		ENSP00000369994.3
B3GALT5	ENST00000475838.1	n.27+99A>G		intron_variant	Intron 1 of 1	5
B3GALT5-AS1	ENST00000839278.1	n.629-27856T>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.779 AC: 32332 AN: 41504

American (AMR) AF: 0.821 AC: 12556 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2659 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4448 AN: 5170

South Asian (SAS) AF: 0.775 AC: 3739 AN: 4826

European-Finnish (FIN) AF: 0.855 AC: 9060 AN: 10600

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52937 AN: 67990

Other (OTH) AF: 0.787 AC: 1660 AN: 2110

Alfa AF: 0.781 Hom.: 76416

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
PhyloP100		-0.63
PromoterAI		0.0069	Neutral
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: rs2837076; hg19: chr21-40928536;