chr2-199812902-C-T

Variant names:

• chr2-199812902-C-T
• rs2030653
• NM_001363886.2:c.398-178G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001363886.2(FTCDNL1):​c.398-178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,226 control chromosomes in the GnomAD database, including 52,129 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 0.83 (52129 hom., cov: 33)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 4 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.879 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	NM_001363886.2	MANE Select	c.398-178G>A		intron	N/A	NP_001350815.1
	FTCDNL1	NM_001350854.2		c.*19+31478G>A		intron	N/A	NP_001337783.1
	FTCDNL1	NM_001350855.2		c.211+33173G>A		intron	N/A	NP_001337784.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	ENST00000420128.6	TSL:5 MANE Select	c.398-178G>A		intron	N/A	ENSP00000457780.1
	FTCDNL1	ENST00000416668.5	TSL:1	c.211+33173G>A		intron	N/A	ENSP00000454447.1
	FTCDNL1	ENST00000881260.1		c.398-178G>A		intron	N/A	ENSP00000551319.1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125736 AN: 152108 Hom.: 52072 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.827 AC: 125852 AN: 152226 Hom.: 52129 Cov.: 33 AF XY: 0.824 AC XY: 61348 AN XY: 74414

African (AFR) AF: 0.854 AC: 35475 AN: 41540

American (AMR) AF: 0.891 AC: 13640 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3102 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4130 AN: 5186

South Asian (SAS) AF: 0.885 AC: 4273 AN: 4828

European-Finnish (FIN) AF: 0.692 AC: 7317 AN: 10576

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55124 AN: 68006

Other (OTH) AF: 0.841 AC: 1777 AN: 2114

Alfa AF: 0.821 Hom.: 181326

Bravo AF: 0.842

Asia WGS AF: 0.843 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		1.3
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: rs2030653; hg19: chr2-200677625;