rs504963

chr19-48705608-G-A

Variant summary

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

The NM_000511.6(FUT2):c.*1620G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 166,932 control chromosomes in the GnomAD database, including 19,219 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 (17914 hom., cov: 32)
  • Exomes 𝑓: 0.41 (1305 hom.)
• Consequence: FUT2 NM_000511.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT2	NM_000511.6	c.*1620G>A		3_prime_UTR_variant	2/2	ENST00000425340.3
FUT2	NM_001097638.3	c.*1620G>A		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT2	ENST00000425340.3	c.*1620G>A		3_prime_UTR_variant	2/2	1	NM_000511.6	P1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71392 AN: 151806 Hom.: 17901 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.487

GnomAD4 exome AF: 0.414 AC: 6214 AN: 15010 Hom.: 1305 Cov.: 0 AF XY: 0.411 AC XY: 2934 AN XY: 7132

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.750

Gnomad4 EAS exome AF: 0.421

Gnomad4 FIN exome AF: 0.413

Gnomad4 NFE exome AF: 0.521

Gnomad4 OTH exome AF: 0.436

GnomAD4 genome AF: 0.470 AC: 71440 AN: 151922 Hom.: 17914 Cov.: 32 AF XY: 0.457 AC XY: 33961 AN XY: 74244

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.00387

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.483

Alfa AF: 0.485 Hom.: 45237

Bravo AF: 0.474

Asia WGS AF: 0.161 AC: 556 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.61
Dann	Benign	0.73

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: rs504963; hg19: chr19-49208865; COSMIC: COSV67179263; COSMIC: COSV67179263;