rs2071699

Variant names:

• chr19-48751247-G-A
• rs2071699
• NM_001384359.1:c.35C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-48751247-G-A
• chr19-48751247-G-C
• chr19-48751247-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_001384359.1(FUT1):​c.35C>T​(p.Ala12Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 1,614,056 control chromosomes in the GnomAD database, including 3,804 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.032 (311 hom., cov: 33)
  • Exomes 𝑓: 0.035 (3493 hom.)
• Consequence: FUT1 NM_001384359.1 missense
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.0240
• Publications: 49 publications found

Genes affected

FUT1 (HGNC:4012): (fucosyltransferase 1 (H blood group)) This gene encodes a Golgi stack membrane protein that is involved in the creation of a precursor of the H antigen, which is required for the final step in the synthesis of soluble A and B antigens. This is one of two genes encoding the galactoside 2-L-fucosyltransferase enzyme. Mutations in this gene are a cause of the H-Bombay blood group. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0031044483).
• BP6: Variant 19-48751247-G-A is Benign according to our data. Variant chr19-48751247-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 3056653.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384359.1. 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
	FUT1	NM_001384359.1	MANE Select	c.35C>T	p.Ala12Val	missense	Exon 2 of 2	NP_001371288.1	Q6IZA2
	FUT1	NM_000148.4		c.35C>T	p.Ala12Val	missense	Exon 4 of 4	NP_000139.1	P19526
	FUT1	NM_001329877.1		c.35C>T	p.Ala12Val	missense	Exon 5 of 5	NP_001316806.1	Q6IZA2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT1	ENST00000645652.2	MANE Select	c.35C>T	p.Ala12Val	missense	Exon 2 of 2	ENSP00000494643.1	P19526
	FUT1	ENST00000927212.1		c.35C>T	p.Ala12Val	missense	Exon 2 of 2	ENSP00000597271.1
	FUT1	ENST00000927213.1		c.35C>T	p.Ala12Val	missense	Exon 2 of 2	ENSP00000597272.1

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4829 AN: 152170 Hom.: 313 Cov.: 33

Gnomad AFR AF: 0.00413

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0272

GnomAD2 exomes AF: 0.0590 AC: 14801 AN: 250760 AF XY: 0.0587

Gnomad AFR exome AF: 0.00315

Gnomad AMR exome AF: 0.0805

Gnomad ASJ exome AF: 0.0279

Gnomad EAS exome AF: 0.282

Gnomad FIN exome AF: 0.0460

Gnomad NFE exome AF: 0.0187

Gnomad OTH exome AF: 0.0486

GnomAD4 exome AF: 0.0346 AC: 50600 AN: 1461768 Hom.: 3493 Cov.: 33 AF XY: 0.0363 AC XY: 26409 AN XY: 727170

African (AFR) AF: 0.00335 AC: 112 AN: 33480

American (AMR) AF: 0.0739 AC: 3302 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 739 AN: 26136

East Asian (EAS) AF: 0.344 AC: 13638 AN: 39694

South Asian (SAS) AF: 0.0996 AC: 8594 AN: 86254

European-Finnish (FIN) AF: 0.0434 AC: 2315 AN: 53364

Middle Eastern (MID) AF: 0.0411 AC: 237 AN: 5766

European-Non Finnish (NFE) AF: 0.0173 AC: 19261 AN: 1111968

Other (OTH) AF: 0.0398 AC: 2402 AN: 60396

GnomAD4 genome AF: 0.0317 AC: 4821 AN: 152288 Hom.: 311 Cov.: 33 AF XY: 0.0358 AC XY: 2669 AN XY: 74464

African (AFR) AF: 0.00411 AC: 171 AN: 41566

American (AMR) AF: 0.0360 AC: 551 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0308 AC: 107 AN: 3472

East Asian (EAS) AF: 0.291 AC: 1502 AN: 5168

South Asian (SAS) AF: 0.113 AC: 542 AN: 4814

European-Finnish (FIN) AF: 0.0447 AC: 475 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0205 AC: 1398 AN: 68034

Other (OTH) AF: 0.0284 AC: 60 AN: 2116

Alfa AF: 0.0246 Hom.: 252

Bravo AF: 0.0302

TwinsUK AF: 0.0154 AC: 57

ALSPAC AF: 0.0187 AC: 72

ESP6500AA AF: 0.00363 AC: 16

ESP6500EA AF: 0.0207 AC: 178

ExAC AF: 0.0572 AC: 6946

Asia WGS AF: 0.182 AC: 630 AN: 3478

EpiCase AF: 0.0192

EpiControl AF: 0.0208

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	FUT1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.65	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.97
DEOGEN2	Benign	0.18	T
Eigen	Benign	-0.83
Eigen_PC	Benign	-0.76
FATHMM_MKL	Benign	0.54	D
LIST_S2	Benign	0.61	T
MetaRNN	Benign	0.0031	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.7	L
PhyloP100		0.024
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.14	N
REVEL	Benign	0.029
Sift	Benign	0.064	T
Sift4G	Benign	1.0	T
Polyphen		0.10	B
Vest4		0.023
MPC		0.43
ClinPred		0.0051	T
GERP RS		-1.3
Varity_R		0.045
gMVP		0.44
Mutation Taster		=98/2	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: rs2071699; hg19: chr19-49254504; COSMIC: COSV55810009; COSMIC: COSV55810009;