rs12373788

Variant names:

• chr2-199768892-G-A
• rs12373788
• ENST00000416668.5:c.212-8057C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.94).
• 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 rank	MANE	Protein	UniProt
FTCDNL1	XR_002959289.2	n.7631C>T		non_coding_transcript_exon_variant	Exon 5 of 5
FTCDNL1	NM_001350854.2	c.*20-8057C>T		intron_variant	Intron 4 of 4		NP_001337783.1
FTCDNL1	NM_001350855.2	c.212-8057C>T		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.212-8057C>T		intron_variant	Intron 3 of 3	1		ENSP00000454447.1
FTCDNL1	ENST00000420922.6	c.*20-8057C>T		intron_variant	Intron 4 of 4	5		ENSP00000456442.1

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

African (AFR) AF: 0.0311 AC: 1291 AN: 41558

American (AMR) AF: 0.0824 AC: 1259 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 296 AN: 3470

East Asian (EAS) AF: 0.184 AC: 948 AN: 5162

South Asian (SAS) AF: 0.0939 AC: 450 AN: 4790

European-Finnish (FIN) AF: 0.298 AC: 3149 AN: 10566

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11080 AN: 67998

Other (OTH) AF: 0.114 AC: 241 AN: 2114

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
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: rs12373788; hg19: chr2-200633615;