rs116089237

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_206965.2(FTCD):c.452A>T(p.Lys151Met) variant causes a missense change. The variant allele was found at a frequency of 0.00459 in 1,562,368 control chromosomes in the GnomAD database, including 260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 120 hom., cov: 34)

Exomes 𝑓: 0.0026 ( 140 hom. )

Consequence

FTCD
NM_206965.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 4.47

Publications

1 publications found

Variant links:

Genes affected

FTCD (HGNC:3974): (formimidoyltransferase cyclodeaminase) The protein encoded by this gene is a bifunctional enzyme that channels 1-carbon units from formiminoglutamate, a metabolite of the histidine degradation pathway, to the folate pool. Mutations in this gene are associated with glutamate formiminotransferase deficiency. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Dec 2009]

FTCD links:

FTCD-AS1 (HGNC:40243): (FTCD antisense RNA 1)

FTCD-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004734993).

BP6

Variant 21-46151896-T-A is Benign according to our data. Variant chr21-46151896-T-A is described in ClinVar as Benign. ClinVar VariationId is 282697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
FTCD	NM_206965.2 link	c.452A>T	p.Lys151Met	missense_variant	Exon 4 of 14	ENST00000397746.8	NP_996848.1
FTCD	NM_001320412.2 link	c.452A>T	p.Lys151Met	missense_variant	Exon 4 of 15		NP_001307341.1
FTCD	NM_006657.3 link	c.452A>T	p.Lys151Met	missense_variant	Exon 4 of 15		NP_006648.1
FTCD-AS1	NR_170989.1 link	n.146+137T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FTCD	ENST00000397746.8 link	c.452A>T	p.Lys151Met	missense_variant	Exon 4 of 14	1	NM_206965.2	ENSP00000380854.3

Frequencies

GnomAD3 genomes

AF:

0.0232

AC:

3536

AN:

152176

Hom.:

120

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0787

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0135

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000500

Gnomad OTH

AF:

0.0148

GnomAD2 exomes

AF:

0.00544

AC:

913

AN:

167830

AF XY:

0.00441

show subpopulations

Gnomad AFR exome

AF:

0.0848

Gnomad AMR exome

AF:

0.00527

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000604

Gnomad OTH exome

AF:

0.00306

GnomAD4 exome

AF:

0.00257

AC:

3622

AN:

1410074

Hom.:

140

Cov.:

AF XY:

0.00225

AC XY:

1568

AN XY:

696976

show subpopulations

African (AFR)

AF:

0.0832

AC:

2679

AN:

32198

American (AMR)

AF:

0.00595

AC:

221

AN:

37156

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25266

East Asian (EAS)

AF:

0.00

AC:

AN:

36750

South Asian (SAS)

AF:

0.000124

AC:

AN:

80790

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48624

Middle Eastern (MID)

AF:

0.00293

AC:

AN:

5122

European-Non Finnish (NFE)

AF:

0.000325

AC:

353

AN:

1085846

Other (OTH)

AF:

0.00590

AC:

344

AN:

58322

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

194

388

581

775

969

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

180

270

360

450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0233

AC:

3544

AN:

152294

Hom.:

120

Cov.:

AF XY:

0.0223

AC XY:

1657

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0787

AC:

3271

AN:

41562

American (AMR)

AF:

0.0135

AC:

206

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.00

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000500

AC:

AN:

68006

Other (OTH)

AF:

0.0147

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

171

342

512

683

854

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00791

Hom.:

Bravo

AF:

0.0270

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0658

AC:

274

ESP6500EA

AF:

0.000361

AC:

ExAC

AF:

0.00554

AC:

645

Asia WGS

AF:

0.00202

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Aug 17, 2015

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Glutamate formiminotransferase deficiency

Benign:1

Jan 24, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.33

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.57

D;.;D;.

Eigen

Uncertain

0.23

Eigen_PC

Benign

0.16

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.93

.;D;D;D

MetaRNN

Benign

0.0047

T;T;T;T

MetaSVM

Benign

-0.58

MutationAssessor

Uncertain

2.2

M;M;M;.

PhyloP100

4.5

PrimateAI

Benign

0.33

PROVEAN

Uncertain

-3.0

D;D;D;D

REVEL

Uncertain

0.42

Sift

Uncertain

0.0020

D;D;D;D

Sift4G

Uncertain

0.0030

D;D;D;D

Polyphen

0.86

P;P;P;P

Vest4

0.47

MVP

0.89

MPC

0.22

ClinPred

0.017

GERP RS

2.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.29

gMVP

0.63

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over