rs8132770

Positions:

• chr21-39653957-A-T

Variant summary

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

The NM_001356336.2(B3GALT5):​c.-160-5796A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,108 control chromosomes in the GnomAD database, including 19,651 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 0.51 (19651 hom., cov: 33)
• Consequence: B3GALT5 NM_001356336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GALT5	NM_001356336.2	c.-160-5796A>T		intron_variant		ENST00000684187.2
B3GALT5	NM_001278650.2	c.-160-5796A>T		intron_variant
B3GALT5	NM_001356338.2	c.-160-5796A>T		intron_variant
B3GALT5	NM_001356339.2	c.-160-5796A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GALT5	ENST00000684187.2	c.-160-5796A>T		intron_variant			NM_001356336.2	P1
	ENST00000416555.1	n.220+23467A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76916 AN: 151990 Hom.: 19633 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.506 AC: 76975 AN: 152108 Hom.: 19651 Cov.: 33 AF XY: 0.509 AC XY: 37846 AN XY: 74354

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.514

Alfa AF: 0.511 Hom.: 2459

Bravo AF: 0.505

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.31

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: rs8132770; hg19: chr21-41025884;