rs2030653

Positions:

• chr2-199812902-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001363886.2(FTCDNL1):​c.398-178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,226 control chromosomes in the GnomAD database, including 52,129 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 0.83 (52129 hom., cov: 33)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FTCDNL1	NM_001363886.2	c.398-178G>A		intron_variant		ENST00000420128.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FTCDNL1	ENST00000420128.6	c.398-178G>A		intron_variant		5	NM_001363886.2
FTCDNL1	ENST00000416668.5	c.211+33173G>A		intron_variant		1
FTCDNL1	ENST00000420922.6	c.*19+31478G>A		intron_variant		5		P1
FTCDNL1	ENST00000642693.1	n.405+6670G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125736 AN: 152108 Hom.: 52072 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.827 AC: 125852 AN: 152226 Hom.: 52129 Cov.: 33 AF XY: 0.824 AC XY: 61348 AN XY: 74414

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.841

Alfa AF: 0.821 Hom.: 81142

Bravo AF: 0.842

Asia WGS AF: 0.843 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.79

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: rs2030653; hg19: chr2-200677625;