2-199850665-T-G

Position:

• chr2-199850665-T-G

Variant summary

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

The NM_001363886.2(FTCDNL1):​c.-8+75A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,302 control chromosomes in the GnomAD database, including 52,362 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 (52305 hom., cov: 32)
  • Exomes 𝑓: 0.90 (57 hom.)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTCDNL1	NM_001363886.2	c.-8+75A>C		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+75A>C		intron_variant		5	NM_001363886.2	ENSP00000457780.1

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125941 AN: 152048 Hom.: 52249 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.846

GnomAD4 exome AF: 0.897 AC: 122 AN: 136 Hom.: 57 AF XY: 0.902 AC XY: 92 AN XY: 102

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.923

Gnomad4 OTH exome AF: 0.625

GnomAD4 genome AF: 0.828 AC: 126054 AN: 152166 Hom.: 52305 Cov.: 32 AF XY: 0.829 AC XY: 61630 AN XY: 74386

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.846

Alfa AF: 0.806 Hom.: 6029

Bravo AF: 0.840

Asia WGS AF: 0.848 AC: 2950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.7
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2949006; hg19: chr2-200715388;