rs17529497

Variant names:

• chr2-199791834-A-G
• rs17529497
• ENST00000416668.5:c.212-30999T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350854.2(FTCDNL1):​c.*20-30999T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,980 control chromosomes in the GnomAD database, including 6,069 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 0.25 (6069 hom., cov: 31)
• Consequence: FTCDNL1 NM_001350854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350854.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	NM_001350854.2		c.*20-30999T>C		intron	N/A	NP_001337783.1	H3BRX2
	FTCDNL1	NM_001350855.2		c.212-30999T>C		intron	N/A	NP_001337784.1	H3BMM2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	ENST00000416668.5	TSL:1	c.212-30999T>C		intron	N/A	ENSP00000454447.1	H3BMM2
	FTCDNL1	ENST00000420922.6	TSL:5	c.*20-30999T>C		intron	N/A	ENSP00000456442.1	H3BRX2
	FTCDNL1	ENST00000642693.1		n.406-6256T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38403 AN: 151862 Hom.: 6068 Cov.: 31

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.253 AC: 38406 AN: 151980 Hom.: 6069 Cov.: 31 AF XY: 0.254 AC XY: 18857 AN XY: 74260

African (AFR) AF: 0.0621 AC: 2576 AN: 41514

American (AMR) AF: 0.267 AC: 4069 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1449 AN: 5172

South Asian (SAS) AF: 0.343 AC: 1646 AN: 4798

European-Finnish (FIN) AF: 0.301 AC: 3167 AN: 10514

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23499 AN: 67926

Other (OTH) AF: 0.246 AC: 519 AN: 2114

Alfa AF: 0.319 Hom.: 9108

Bravo AF: 0.237

Asia WGS AF: 0.316 AC: 1095 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-0.093
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17529497; hg19: chr2-200656557;