rs10854398

Variant names:

• chr21-39649825-T-C
• rs10854398
• NM_001356336.2:c.-161+3203T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001356336.2(B3GALT5):​c.-161+3203T>C 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 151,894 control chromosomes in the GnomAD database, including 19,590 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 (19590 hom., cov: 31)
• Consequence: B3GALT5 NM_001356336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.57
• Publications: 8 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

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.-161+3203T>C		intron	N/A	NP_001343265.1	Q9Y2C3
	B3GALT5	NM_001278650.2		c.-160-9928T>C		intron	N/A	NP_001265579.1	Q9Y2C3
	B3GALT5	NM_001356338.2		c.-161+3203T>C		intron	N/A	NP_001343267.1	Q9Y2C3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT5	ENST00000684187.2	MANE Select	c.-161+3203T>C		intron	N/A	ENSP00000506797.1	Q9Y2C3
	B3GALT5	ENST00000380620.8	TSL:1	c.-161+3203T>C		intron	N/A	ENSP00000369994.3	Q9Y2C3
	B3GALT5	ENST00000343118.6	TSL:5	c.-161+7349T>C		intron	N/A	ENSP00000343318.4	Q9Y2C3

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76733 AN: 151776 Hom.: 19572 Cov.: 31

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.514

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: 76793 AN: 151894 Hom.: 19590 Cov.: 31 AF XY: 0.509 AC XY: 37785 AN XY: 74230

African (AFR) AF: 0.471 AC: 19495 AN: 41394

American (AMR) AF: 0.554 AC: 8465 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2266 AN: 5158

South Asian (SAS) AF: 0.515 AC: 2474 AN: 4800

European-Finnish (FIN) AF: 0.543 AC: 5727 AN: 10542

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34936 AN: 67938

Other (OTH) AF: 0.515 AC: 1086 AN: 2110

Alfa AF: 0.511 Hom.: 51826

Bravo AF: 0.505

Asia WGS AF: 0.551 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.51
PhyloP100		-3.6
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: rs10854398; hg19: chr21-41021752;