2-199783496-T-C

Variant names:

• chr2-199783496-T-C
• rs12473679
• ENST00000416668.5:c.212-22661A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416668.5(FTCDNL1):​c.212-22661A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,096 control chromosomes in the GnomAD database, including 17,674 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 0.45 (17674 hom., cov: 32)
• Consequence: FTCDNL1 ENST00000416668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FTCDNL1	XM_047444170.1	c.*298A>G		3_prime_UTR_variant	Exon 4 of 4		XP_047300126.1
FTCDNL1	NM_001350854.2	c.*20-22661A>G		intron_variant	Intron 4 of 4		NP_001337783.1
FTCDNL1	NM_001350855.2	c.212-22661A>G		intron_variant	Intron 3 of 3		NP_001337784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000416668.5	c.212-22661A>G		intron_variant	Intron 3 of 3	1		ENSP00000454447.1
FTCDNL1	ENST00000420922.6	c.*20-22661A>G		intron_variant	Intron 4 of 4	5		ENSP00000456442.1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68615 AN: 151978 Hom.: 17674 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.451 AC: 68622 AN: 152096 Hom.: 17674 Cov.: 32 AF XY: 0.459 AC XY: 34124 AN XY: 74338

African (AFR) AF: 0.198 AC: 8218 AN: 41500

American (AMR) AF: 0.442 AC: 6758 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3468

East Asian (EAS) AF: 0.541 AC: 2787 AN: 5154

South Asian (SAS) AF: 0.545 AC: 2627 AN: 4822

European-Finnish (FIN) AF: 0.668 AC: 7055 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38188 AN: 67982

Other (OTH) AF: 0.436 AC: 920 AN: 2112

Alfa AF: 0.509 Hom.: 6887

Bravo AF: 0.419

Asia WGS AF: 0.538 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		-0.69
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: rs12473679; hg19: chr2-200648219;