rs12373788

Positions:

• chr2-199768892-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416668.5(FTCDNL1):​c.212-8057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,148 control chromosomes in the GnomAD database, including 1,561 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 0.12 (1561 hom., cov: 32)
• Consequence: FTCDNL1 ENST00000416668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FTCDNL1	NM_001350854.2	c.*20-8057C>T		intron_variant
FTCDNL1	NM_001350855.2	c.212-8057C>T		intron_variant
FTCDNL1	XM_024452852.2	c.397+50680C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FTCDNL1	ENST00000416668.5	c.212-8057C>T		intron_variant		1
FTCDNL1	ENST00000420922.6	c.*20-8057C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18903 AN: 152030 Hom.: 1562 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.124 AC: 18895 AN: 152148 Hom.: 1561 Cov.: 32 AF XY: 0.129 AC XY: 9559 AN XY: 74352

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.0824

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.0939

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.114

Alfa AF: 0.153 Hom.: 249

Bravo AF: 0.105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.86
DANN	Benign	0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs12373788; hg19: chr2-200633615;