rs13008446

Positions:

• chr2-199763777-G-A
• chr2-199763777-G-C

Variant summary

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

The NM_001350854.2(FTCDNL1):​c.*20-2942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,196 control chromosomes in the GnomAD database, including 23,117 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 0.50 (23117 hom., cov: 33)
• Consequence: FTCDNL1 NM_001350854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

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]

FTCDNL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTCDNL1	NM_001350854.2	c.*20-2942C>T		intron_variant			NP_001337783.1
FTCDNL1	NM_001350855.2	c.212-2942C>T		intron_variant			NP_001337784.1
FTCDNL1	XM_024452852.2	c.397+55795C>T		intron_variant			XP_024308620.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000416668.5	c.212-2942C>T		intron_variant		1		ENSP00000454447.1
FTCDNL1	ENST00000420922.6	c.*20-2942C>T		intron_variant		5		ENSP00000456442.1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76562 AN: 152078 Hom.: 23118 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.503 AC: 76573 AN: 152196 Hom.: 23117 Cov.: 33 AF XY: 0.511 AC XY: 38052 AN XY: 74422

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.498

Alfa AF: 0.615 Hom.: 13687

Bravo AF: 0.463

Asia WGS AF: 0.575 AC: 2000 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	1.5
DANN	Benign	0.49

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: rs13008446; hg19: chr2-200628500;