21-39644661-T-A

Variant names:

• chr21-39644661-T-A
• rs609145
• NM_001356336.2:c.-391-1731T>A

Variant summary

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

The NM_001356336.2(B3GALT5):​c.-391-1731T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,094 control chromosomes in the GnomAD database, including 21,874 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 0.53 (21874 hom., cov: 33)
• Consequence: B3GALT5 NM_001356336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 3 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=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.581 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT5	NM_001356336.2	MANE Select	c.-391-1731T>A		intron	N/A	NP_001343265.1
	B3GALT5	NM_001278650.2		c.-160-15092T>A		intron	N/A	NP_001265579.1
	B3GALT5	NM_001356338.2		c.-391-1731T>A		intron	N/A	NP_001343267.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT5	ENST00000684187.2	MANE Select	c.-391-1731T>A		intron	N/A	ENSP00000506797.1
	B3GALT5	ENST00000380620.8	TSL:1	c.-391-1731T>A		intron	N/A	ENSP00000369994.3
	B3GALT5	ENST00000343118.6	TSL:5	c.-161+2185T>A		intron	N/A	ENSP00000343318.4

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81281 AN: 151976 Hom.: 21842 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.535 AC: 81363 AN: 152094 Hom.: 21874 Cov.: 33 AF XY: 0.534 AC XY: 39681 AN XY: 74368

African (AFR) AF: 0.579 AC: 24034 AN: 41486

American (AMR) AF: 0.513 AC: 7838 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3468

East Asian (EAS) AF: 0.521 AC: 2689 AN: 5158

South Asian (SAS) AF: 0.599 AC: 2886 AN: 4820

European-Finnish (FIN) AF: 0.464 AC: 4912 AN: 10590

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35407 AN: 67978

Other (OTH) AF: 0.538 AC: 1134 AN: 2108

Alfa AF: 0.370 Hom.: 923

Bravo AF: 0.536

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.22
PhyloP100		-0.77
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: rs609145; hg19: chr21-41016588;