rs2837108

Variant names:

• chr21-39659683-C-G
• rs2837108
• NM_001356336.2:c.-160-70C>G

Your query was ambiguous. Multiple possible variants found:

• chr21-39659683-C-G
• chr21-39659683-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001356336.2(B3GALT5):​c.-160-70C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: B3GALT5 NM_001356336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 9 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001356336.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT5	NM_001356336.2	MANE Select	c.-160-70C>G		intron	N/A	NP_001343265.1	Q9Y2C3
	B3GALT5	NM_033172.3		c.13-877C>G		intron	N/A	NP_149362.2	A0A0A0MS93
	B3GALT5	NM_001278650.2		c.-160-70C>G		intron	N/A	NP_001265579.1	Q9Y2C3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT5	ENST00000684187.2	MANE Select	c.-160-70C>G		intron	N/A	ENSP00000506797.1	Q9Y2C3
	B3GALT5	ENST00000380618.5	TSL:1	c.-160-70C>G		intron	N/A	ENSP00000369992.1	Q9Y2C3
	B3GALT5	ENST00000380620.8	TSL:1	c.-160-70C>G		intron	N/A	ENSP00000369994.3	Q9Y2C3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 735114 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 342150

African (AFR) AF: 0.00 AC: 0 AN: 13778

American (AMR) AF: 0.00 AC: 0 AN: 860

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4568

East Asian (EAS) AF: 0.00 AC: 0 AN: 3174

South Asian (SAS) AF: 0.00 AC: 0 AN: 14440

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 250

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1458

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 672622

Other (OTH) AF: 0.00 AC: 0 AN: 23964

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 26633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		0.11

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: rs2837108; hg19: chr21-41031610;