rs12470986

Variant names:

• chr2-199830055-G-C
• rs12470986
• NM_001363886.2:c.212-10298C>G

Variant summary

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

The NM_001363886.2(FTCDNL1):​c.212-10298C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 151,260 control chromosomes in the GnomAD database, including 335 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 0.042 (335 hom., cov: 32)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FTCDNL1	NM_001363886.2	c.212-10298C>G		intron_variant	Intron 3 of 4	ENST00000420128.6	NP_001350815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000420128.6	c.212-10298C>G		intron_variant	Intron 3 of 4	5	NM_001363886.2	ENSP00000457780.1

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6403 AN: 151148 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00483

Gnomad OTH AF: 0.0423

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

GnomAD4 genome AF: 0.0424 AC: 6420 AN: 151260 Hom.: 335 Cov.: 32 AF XY: 0.0447 AC XY: 3303 AN XY: 73900

African (AFR) AF: 0.0733 AC: 3025 AN: 41242

American (AMR) AF: 0.130 AC: 1968 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 9 AN: 3460

East Asian (EAS) AF: 0.126 AC: 651 AN: 5154

South Asian (SAS) AF: 0.0471 AC: 225 AN: 4772

European-Finnish (FIN) AF: 0.0106 AC: 110 AN: 10388

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00484 AC: 328 AN: 67762

Other (OTH) AF: 0.0448 AC: 94 AN: 2100

Alfa AF: 0.0253 Hom.: 25

Bravo AF: 0.0550

Asia WGS AF: 0.0920 AC: 318 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.56
PhyloP100		0.14
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: rs12470986; hg19: chr2-200694778;