2-199791498-T-C

Variant names:

• chr2-199791498-T-C
• rs6759644
• ENST00000416668.5:c.212-30663A>G

Variant summary

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

The ENST00000416668.5(FTCDNL1):​c.212-30663A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,918 control chromosomes in the GnomAD database, including 26,014 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 0.58 (26014 hom., cov: 32)
• Consequence: FTCDNL1 ENST00000416668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 2 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=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416668.5. 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_001350854.2		c.*20-30663A>G		intron	N/A	NP_001337783.1
	FTCDNL1	NM_001350855.2		c.212-30663A>G		intron	N/A	NP_001337784.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	ENST00000416668.5	TSL:1	c.212-30663A>G		intron	N/A	ENSP00000454447.1
	FTCDNL1	ENST00000420922.6	TSL:5	c.*20-30663A>G		intron	N/A	ENSP00000456442.1
	FTCDNL1	ENST00000642693.1		n.406-5920A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87511 AN: 151800 Hom.: 25985 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.577 AC: 87589 AN: 151918 Hom.: 26014 Cov.: 32 AF XY: 0.585 AC XY: 43432 AN XY: 74234

African (AFR) AF: 0.470 AC: 19480 AN: 41406

American (AMR) AF: 0.657 AC: 10036 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1747 AN: 3468

East Asian (EAS) AF: 0.843 AC: 4365 AN: 5180

South Asian (SAS) AF: 0.613 AC: 2956 AN: 4826

European-Finnish (FIN) AF: 0.686 AC: 7216 AN: 10514

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40204 AN: 67922

Other (OTH) AF: 0.540 AC: 1140 AN: 2110

Alfa AF: 0.539 Hom.: 2463

Bravo AF: 0.568

Asia WGS AF: 0.737 AC: 2557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.71
PhyloP100		1.0
Mutation Taster		=95/5	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: rs6759644; hg19: chr2-200656221;