rs632111

Variant names:

• chr19-48705721-A-G
• rs632111
• NM_000511.6:c.*1733A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-48705721-A-G
• chr19-48705721-A-T

Variant summary

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

The NM_000511.6(FUT2):​c.*1733A>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 0.442 in 166,880 control chromosomes in the GnomAD database, including 17,310 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 0.44 (15995 hom., cov: 31)
  • Exomes 𝑓: 0.42 (1315 hom.)
• Consequence: FUT2 NM_000511.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 41 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]

MAMSTR (HGNC:26689): (MEF2 activating motif and SAP domain containing transcriptional regulator) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of myotube differentiation and positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 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.*1733A>G		3_prime_UTR	Exon 2 of 2	NP_000502.4	A8K2L2
	FUT2	NM_001097638.3		c.*1733A>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.*1733A>G		3_prime_UTR	Exon 2 of 2	ENSP00000387498.2	Q10981

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67568 AN: 151780 Hom.: 16002 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.416 AC: 6237 AN: 14984 Hom.: 1315 Cov.: 0 AF XY: 0.413 AC XY: 2942 AN XY: 7116

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.415 AC: 54 AN: 130

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.415 AC: 6094 AN: 14670

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.536 AC: 45 AN: 84

Other (OTH) AF: 0.433 AC: 39 AN: 90

GnomAD4 genome AF: 0.445 AC: 67570 AN: 151896 Hom.: 15995 Cov.: 31 AF XY: 0.433 AC XY: 32140 AN XY: 74210

African (AFR) AF: 0.457 AC: 18940 AN: 41454

American (AMR) AF: 0.378 AC: 5761 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3472

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5164

South Asian (SAS) AF: 0.296 AC: 1406 AN: 4742

European-Finnish (FIN) AF: 0.406 AC: 4281 AN: 10538

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

European-Non Finnish (NFE) AF: 0.501 AC: 34057 AN: 67958

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.469 Hom.: 38206

Bravo AF: 0.445

Asia WGS AF: 0.137 AC: 474 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.80
PhyloP100		0.27
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: rs632111; hg19: chr19-49208978; COSMIC: COSV67179234; COSMIC: COSV67179234;