21-39651564-A-G

Variant names:

• chr21-39651564-A-G
• rs596958
• NM_001356336.2:c.-161+4942A>G

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+4942A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 152,344 control chromosomes in the GnomAD database, including 69,547 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 0.96 (69547 hom., cov: 34)
• Consequence: B3GALT5 NM_001356336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 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+4942A>G		intron	N/A	NP_001343265.1	Q9Y2C3
	B3GALT5	NM_001278650.2		c.-160-8189A>G		intron	N/A	NP_001265579.1	Q9Y2C3
	B3GALT5	NM_001356338.2		c.-161+4942A>G		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+4942A>G		intron	N/A	ENSP00000506797.1	Q9Y2C3
	B3GALT5	ENST00000380620.8	TSL:1	c.-161+4942A>G		intron	N/A	ENSP00000369994.3	Q9Y2C3
	B3GALT5	ENST00000343118.6	TSL:5	c.-160-8189A>G		intron	N/A	ENSP00000343318.4	Q9Y2C3

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145377 AN: 152226 Hom.: 69490 Cov.: 34

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.955 AC: 145494 AN: 152344 Hom.: 69547 Cov.: 34 AF XY: 0.956 AC XY: 71214 AN XY: 74496

African (AFR) AF: 0.988 AC: 41095 AN: 41586

American (AMR) AF: 0.918 AC: 14052 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3303 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5174

South Asian (SAS) AF: 0.984 AC: 4747 AN: 4826

European-Finnish (FIN) AF: 0.947 AC: 10061 AN: 10620

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63846 AN: 68042

Other (OTH) AF: 0.966 AC: 2043 AN: 2116

Alfa AF: 0.943 Hom.: 28988

Bravo AF: 0.954

Asia WGS AF: 0.991 AC: 3446 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	2.6
DANN	Benign	0.52
PhyloP100		0.14
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: rs596958; hg19: chr21-41023491;