Variant 21-46155458-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_206965.2(FTCD):c.54+12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,607,302 control chromosomes in the GnomAD database, including 89,941 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 8095 hom., cov: 34)

Exomes 𝑓: 0.32 ( 81846 hom. )

Consequence

FTCD
NM_206965.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.158

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 (HGNC:):

FTCD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 21-46155458-C-T is Benign according to our data. Variant chr21-46155458-C-T is described in ClinVar as [Benign]. Clinvar id is 95427.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
FTCD	NM_206965.2 linkuse as main transcript	c.54+12G>A	intron_variant	ENST00000397746.8	NP_996848.1	O95954-1
FTCD	NM_001320412.2 linkuse as main transcript	c.54+12G>A	intron_variant		NP_001307341.1	O95954-2
FTCD	NM_006657.3 linkuse as main transcript	c.54+12G>A	intron_variant		NP_006648.1	O95954-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTCD	ENST00000397746.8 linkuse as main transcript	c.54+12G>A		intron_variant		1	NM_206965.2	ENSP00000380854.3		O95954-1

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43503

AN:

152058

Hom.:

8085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.797

Gnomad SAS

AF:

0.463

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.286

Gnomad OTH

AF:

0.289

GnomAD3 exomes

AF:

0.383

AC:

95432

AN:

249248

Hom.:

22563

AF XY:

0.378

AC XY:

51142

AN XY:

135298

show subpopulations

Gnomad AFR exome

AF:

0.108

Gnomad AMR exome

AF:

0.606

Gnomad ASJ exome

AF:

0.253

Gnomad EAS exome

AF:

0.823

Gnomad SAS exome

AF:

0.452

Gnomad FIN exome

AF:

0.386

Gnomad NFE exome

AF:

0.277

Gnomad OTH exome

AF:

0.338

GnomAD4 exome

AF:

0.315

AC:

458499

AN:

1455126

Hom.:

81846

Cov.:

AF XY:

0.318

AC XY:

229932

AN XY:

724190

show subpopulations

Gnomad4 AFR exome

AF:

0.107

Gnomad4 AMR exome

AF:

0.589

Gnomad4 ASJ exome

AF:

0.256

Gnomad4 EAS exome

AF:

0.789

Gnomad4 SAS exome

AF:

0.447

Gnomad4 FIN exome

AF:

0.378

Gnomad4 NFE exome

AF:

0.282

Gnomad4 OTH exome

AF:

0.313

GnomAD4 genome

AF:

0.286

AC:

43511

AN:

152176

Hom.:

8095

Cov.:

AF XY:

0.301

AC XY:

22411

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.454

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.797

Gnomad4 SAS

AF:

0.462

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.286

Gnomad4 OTH

AF:

0.286

Alfa

AF:

0.288

Hom.:

8155

Bravo

AF:

0.284

Asia WGS

AF:

0.556

AC:

1931

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

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Jan 30, 2018

- -

Glutamate formiminotransferase deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.0

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over