rs2837108

chr21-39659683-C-Tchr21-39659683-C-G

Variant summary

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

The NM_001356336.2(B3GALT5):c.-160-70C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 884,472 control chromosomes in the GnomAD database, including 85,051 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 0.35 (10961 hom., cov: 31)
  • Exomes 𝑓: 0.44 (74090 hom.)
• Consequence: B3GALT5 NM_001356336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GALT5	NM_001356336.2	c.-160-70C>T		intron_variant		ENST00000684187.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GALT5	ENST00000684187.2	c.-160-70C>T		intron_variant			NM_001356336.2	P1
	ENST00000416555.1	n.220+29193C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52570 AN: 151400 Hom.: 10961 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.385

GnomAD4 exome AF: 0.445 AC: 325909 AN: 733004 Hom.: 74090 AF XY: 0.446 AC XY: 152240 AN XY: 341268

Gnomad4 AFR exome AF: 0.0976

Gnomad4 AMR exome AF: 0.334

Gnomad4 ASJ exome AF: 0.520

Gnomad4 EAS exome AF: 0.0769

Gnomad4 SAS exome AF: 0.434

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.454

Gnomad4 OTH exome AF: 0.421

GnomAD4 genome AF: 0.347 AC: 52571 AN: 151468 Hom.: 10961 Cov.: 31 AF XY: 0.351 AC XY: 25941 AN XY: 73948

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.0756

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.383

Alfa AF: 0.442 Hom.: 20265

Bravo AF: 0.327

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.8
Dann	Benign	0.69

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: rs2837108; hg19: chr21-41031610;