rs58319901

chr2-199833224-G-Achr2-199833224-G-Cchr2-199833224-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363886.2(FTCDNL1):c.211+12851C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,956 control chromosomes in the GnomAD database, including 5,957 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 0.25 (5957 hom., cov: 32)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

FTCDNL1 (HGNC:48661): (formiminotransferase cyclodeaminase N-terminal like) Predicted to enable folic acid binding activity and transferase activity. [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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FTCDNL1	NM_001363886.2	c.211+12851C>T		intron_variant		ENST00000420128.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FTCDNL1	ENST00000420128.6	c.211+12851C>T		intron_variant		5	NM_001363886.2

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38696 AN: 151838 Hom.: 5952 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.246

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38707 AN: 151956 Hom.: 5957 Cov.: 32 AF XY: 0.262 AC XY: 19466 AN XY: 74260

Gnomad4 AFR AF: 0.0821

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.250

Alfa AF: 0.285 Hom.: 886

Bravo AF: 0.239

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.27

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: rs58319901; hg19: chr2-200697947;