2-199850043-C-T

Position:

• chr2-199850043-C-T

Variant summary

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

The NM_001363886.2(FTCDNL1):​c.-8+697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 151,972 control chromosomes in the GnomAD database, including 34,825 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 0.67 (34825 hom., cov: 31)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTCDNL1	NM_001363886.2	c.-8+697G>A		intron_variant		ENST00000420128.6	NP_001350815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000420128.6	c.-8+697G>A		intron_variant		5	NM_001363886.2	ENSP00000457780

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102348 AN: 151852 Hom.: 34777 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.674 AC: 102458 AN: 151972 Hom.: 34825 Cov.: 31 AF XY: 0.680 AC XY: 50530 AN XY: 74264

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.652

Alfa AF: 0.647 Hom.: 3978

Bravo AF: 0.679

Asia WGS AF: 0.800 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
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: rs717915; hg19: chr2-200714766;