rs12615435

Variant names:

• chr2-199773786-T-G
• rs12615435
• ENST00000416668.5:c.212-12951A>C

Variant summary

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

The ENST00000416668.5(FTCDNL1):​c.212-12951A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 152,282 control chromosomes in the GnomAD database, including 551 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 0.076 (551 hom., cov: 32)
• Consequence: FTCDNL1 ENST00000416668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.823
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FTCDNL1	XR_002959289.2	n.2737A>C		non_coding_transcript_exon_variant	Exon 5 of 5
FTCDNL1	NM_001350854.2	c.*20-12951A>C		intron_variant	Intron 4 of 4		NP_001337783.1
FTCDNL1	NM_001350855.2	c.212-12951A>C		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.212-12951A>C		intron_variant	Intron 3 of 3	1		ENSP00000454447.1
FTCDNL1	ENST00000420922.6	c.*20-12951A>C		intron_variant	Intron 4 of 4	5		ENSP00000456442.1

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11474 AN: 152164 Hom.: 544 Cov.: 32

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0992

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0755 AC: 11504 AN: 152282 Hom.: 551 Cov.: 32 AF XY: 0.0756 AC XY: 5631 AN XY: 74454

African (AFR) AF: 0.0456 AC: 1897 AN: 41576

American (AMR) AF: 0.0994 AC: 1520 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5172

South Asian (SAS) AF: 0.0452 AC: 218 AN: 4826

European-Finnish (FIN) AF: 0.0747 AC: 793 AN: 10618

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0785 AC: 5341 AN: 68010

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0824 Hom.: 1874

Bravo AF: 0.0778

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		0.82
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: rs12615435; hg19: chr2-200638509;