2-199833224-G-A

Variant names:

• chr2-199833224-G-A
• rs58319901
• NM_001363886.2:c.211+12851C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363886.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	NM_001363886.2	MANE Select	c.211+12851C>T		intron	N/A	NP_001350815.1
	FTCDNL1	NM_001350853.2		c.211+12851C>T		intron	N/A	NP_001337782.1
	FTCDNL1	NM_001350854.2		c.*19+11156C>T		intron	N/A	NP_001337783.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	ENST00000420128.6	TSL:5 MANE Select	c.211+12851C>T		intron	N/A	ENSP00000457780.1
	FTCDNL1	ENST00000622774.2	TSL:1	c.211+12851C>T		intron	N/A	ENSP00000482786.1
	FTCDNL1	ENST00000416668.5	TSL:1	c.211+12851C>T		intron	N/A	ENSP00000454447.1

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

African (AFR) AF: 0.0821 AC: 3403 AN: 41450

American (AMR) AF: 0.308 AC: 4706 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1195 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1868 AN: 5156

South Asian (SAS) AF: 0.415 AC: 1993 AN: 4808

European-Finnish (FIN) AF: 0.338 AC: 3556 AN: 10532

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21242 AN: 67954

Other (OTH) AF: 0.250 AC: 527 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.27
PhyloP100		-0.20
Mutation Taster		=100/0	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: rs58319901; hg19: chr2-200697947;