chr2-199831723-T-C

Position:

• chr2-199831723-T-C

Variant summary

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

The NM_001363886.2(FTCDNL1):​c.212-11966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,982 control chromosomes in the GnomAD database, including 2,267 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 0.16 (2267 hom., cov: 32)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTCDNL1	NM_001363886.2	c.212-11966A>G		intron_variant		ENST00000420128.6	NP_001350815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000420128.6	c.212-11966A>G		intron_variant		5	NM_001363886.2	ENSP00000457780

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24490 AN: 151864 Hom.: 2266 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.161 AC: 24524 AN: 151982 Hom.: 2267 Cov.: 32 AF XY: 0.162 AC XY: 12069 AN XY: 74274

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.185

Alfa AF: 0.140 Hom.: 1482

Bravo AF: 0.180

Asia WGS AF: 0.203 AC: 704 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.44
DANN	Benign	0.39

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: rs10203122; hg19: chr2-200696446;