rs504963

Variant names:

• chr19-48705608-G-A
• rs504963
• NM_000511.6:c.*1620G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-48705608-G-A
• chr19-48705608-G-C
• chr19-48705608-G-T

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]

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

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 rank	MANE	Protein	UniProt
FUT2	NM_000511.6	c.*1620G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000425340.3	NP_000502.4
FUT2	NM_001097638.3	c.*1620G>A		3_prime_UTR_variant	Exon 2 of 2		NP_001091107.1
MAMSTR	XM_047438640.1	c.*1660C>T		downstream_gene_variant			XP_047294596.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT2	ENST00000425340.3	c.*1620G>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_000511.6	ENSP00000387498.2

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;