rs485073

Variant names:

• chr19-48703998-A-G
• rs485073
• NM_000511.6:c.*10A>G

Variant summary

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

The NM_000511.6(FUT2):​c.*10A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,607,944 control chromosomes in the GnomAD database, including 200,299 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 0.47 (17456 hom., cov: 32)
  • Exomes 𝑓: 0.49 (182843 hom.)
• Consequence: FUT2 NM_000511.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 25 publications found

Genes affected

FUT2 (HGNC:4013): (fucosyltransferase 2 (H blood group)) This gene is one of two encoding the galactoside 2-L-fucosyltransferase enzyme. The encoded protein is important for the final step in the soluble ABO blood group antigen synthesis pathway. It is also involved in cell-cell interaction, cell surface expression, and cell proliferation. Mutations in this gene are a cause of the H-Bombay blood group where red blood cells lack the H antigen. [provided by RefSeq, May 2022]

LOC105447645 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT2	NM_000511.6	c.*10A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000425340.3	NP_000502.4
FUT2	NM_001097638.3	c.*10A>G		3_prime_UTR_variant	Exon 2 of 2		NP_001091107.1
LOC105447645	NR_131188.1	n.-150T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT2	ENST00000425340.3	c.*10A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_000511.6	ENSP00000387498.2
FUT2	ENST00000522966.2	c.*10A>G		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000430227.2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70521 AN: 151492 Hom.: 17460 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.479

GnomAD2 exomes AF: 0.404 AC: 101026 AN: 249890 AF XY: 0.407

Gnomad AFR exome AF: 0.520

Gnomad AMR exome AF: 0.279

Gnomad ASJ exome AF: 0.476

Gnomad EAS exome AF: 0.00431

Gnomad FIN exome AF: 0.417

Gnomad NFE exome AF: 0.503

Gnomad OTH exome AF: 0.456

GnomAD4 exome AF: 0.486 AC: 707951 AN: 1456336 Hom.: 182843 Cov.: 36 AF XY: 0.481 AC XY: 348260 AN XY: 724614

African (AFR) AF: 0.525 AC: 17536 AN: 33396

American (AMR) AF: 0.293 AC: 13069 AN: 44672

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 12330 AN: 26122

East Asian (EAS) AF: 0.00242 AC: 96 AN: 39660

South Asian (SAS) AF: 0.322 AC: 27553 AN: 85662

European-Finnish (FIN) AF: 0.422 AC: 22392 AN: 53112

Middle Eastern (MID) AF: 0.541 AC: 3110 AN: 5752

European-Non Finnish (NFE) AF: 0.526 AC: 582603 AN: 1107812

Other (OTH) AF: 0.486 AC: 29262 AN: 60148

GnomAD4 genome AF: 0.465 AC: 70533 AN: 151608 Hom.: 17456 Cov.: 32 AF XY: 0.453 AC XY: 33545 AN XY: 74050

African (AFR) AF: 0.521 AC: 21549 AN: 41342

American (AMR) AF: 0.386 AC: 5883 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3468

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5166

South Asian (SAS) AF: 0.296 AC: 1399 AN: 4732

European-Finnish (FIN) AF: 0.408 AC: 4280 AN: 10482

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34271 AN: 67860

Other (OTH) AF: 0.475 AC: 1003 AN: 2110

Alfa AF: 0.501 Hom.: 9973

Bravo AF: 0.468

Asia WGS AF: 0.157 AC: 543 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.28
PhyloP100		-0.57
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: rs485073; hg19: chr19-49207255;