NM_000511.6:c.*193T>G

Variant names:

• chr19-48704181-T-G
• rs281376
• NM_000511.6:c.*193T>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.*193T>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 0.999 in 152,040 control chromosomes in the GnomAD database, including 75,838 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 1.0 (75838 hom., cov: 30)
  • Exomes 𝑓: 1.0 (257352 hom.)
  • Failed GnomAD Quality Control
• Consequence: FUT2 NM_000511.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 6 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000511.6. 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
	FUT2	NM_000511.6	MANE Select	c.*193T>G		3_prime_UTR	Exon 2 of 2	NP_000502.4	A8K2L2
	FUT2	NM_001097638.3		c.*193T>G		3_prime_UTR	Exon 2 of 2	NP_001091107.1	Q10981

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT2	ENST00000425340.3	TSL:1 MANE Select	c.*193T>G		3_prime_UTR	Exon 2 of 2	ENSP00000387498.2	Q10981
	FUT2	ENST00000522966.2	TSL:2	c.*193T>G		3_prime_UTR	Exon 2 of 2	ENSP00000430227.2	Q10981
	FUT2	ENST00000960751.1		c.*193T>G		3_prime_UTR	Exon 3 of 3	ENSP00000630810.1

Frequencies

GnomAD3 genomes AF: 0.999 AC: 151735 AN: 151924 Hom.: 75779 Cov.: 30

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.999

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.999

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.999 AC: 515266 AN: 515856 Hom.: 257352 Cov.: 5 AF XY: 0.999 AC XY: 272457 AN XY: 272742

African (AFR) AF: 1.00 AC: 14704 AN: 14704

American (AMR) AF: 1.00 AC: 30600 AN: 30604

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 16018 AN: 16018

East Asian (EAS) AF: 0.985 AC: 30519 AN: 30982

South Asian (SAS) AF: 1.00 AC: 52631 AN: 52644

European-Finnish (FIN) AF: 1.00 AC: 43727 AN: 43728

Middle Eastern (MID) AF: 1.00 AC: 2118 AN: 2118

European-Non Finnish (NFE) AF: 1.00 AC: 297230 AN: 297236

Other (OTH) AF: 0.996 AC: 27719 AN: 27822

GnomAD4 genome AF: 0.999 AC: 151852 AN: 152040 Hom.: 75838 Cov.: 30 AF XY: 0.999 AC XY: 74208 AN XY: 74300

African (AFR) AF: 1.00 AC: 41516 AN: 41518

American (AMR) AF: 0.999 AC: 15236 AN: 15258

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5004 AN: 5160

South Asian (SAS) AF: 0.999 AC: 4705 AN: 4708

European-Finnish (FIN) AF: 1.00 AC: 10602 AN: 10602

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68006 AN: 68008

Other (OTH) AF: 0.999 AC: 2105 AN: 2108

Alfa AF: 1.00 Hom.: 9252

Bravo AF: 0.999

Asia WGS AF: 0.989 AC: 3377 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-1.1
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: rs281376; hg19: chr19-49207438;