rs10931875

chr2-199777654-C-Achr2-199777654-C-T

Variant summary

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

The ENST00000416668.5(FTCDNL1):c.212-16819G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,580 control chromosomes in the GnomAD database, including 23,188 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 0.54 (23188 hom., cov: 32)
• Consequence: FTCDNL1 ENST00000416668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FTCDNL1	NM_001350854.2	c.*20-16819G>T		intron_variant
FTCDNL1	NM_001350855.2	c.212-16819G>T		intron_variant
FTCDNL1	XM_024452852.2	c.397+41918G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FTCDNL1	ENST00000416668.5	c.212-16819G>T		intron_variant		1
FTCDNL1	ENST00000420922.6	c.*20-16819G>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82443 AN: 151462 Hom.: 23172 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.544 AC: 82484 AN: 151580 Hom.: 23188 Cov.: 32 AF XY: 0.552 AC XY: 40851 AN XY: 74056

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.519

Alfa AF: 0.583 Hom.: 3279

Bravo AF: 0.531

Asia WGS AF: 0.639 AC: 2219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.9
Dann	Benign	0.62

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: rs10931875; hg19: chr2-200642377;