rs7572473

Variant names:

• chr2-199770194-C-A
• rs7572473
• ENST00000416668.5:c.212-9359G>T

Variant summary

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

The XR_002959289.2(FTCDNL1):​n.6329G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,122 control chromosomes in the GnomAD database, including 32,422 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 0.60 (32422 hom., cov: 32)
• Consequence: FTCDNL1 XR_002959289.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 11 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FTCDNL1	XR_002959289.2	n.6329G>T		non_coding_transcript_exon_variant	Exon 5 of 5
FTCDNL1	NM_001350854.2	c.*20-9359G>T		intron_variant	Intron 4 of 4		NP_001337783.1
FTCDNL1	NM_001350855.2	c.212-9359G>T		intron_variant	Intron 3 of 3		NP_001337784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000416668.5	c.212-9359G>T		intron_variant	Intron 3 of 3	1		ENSP00000454447.1
FTCDNL1	ENST00000420922.6	c.*20-9359G>T		intron_variant	Intron 4 of 4	5		ENSP00000456442.1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91921 AN: 152004 Hom.: 32426 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.604 AC: 91922 AN: 152122 Hom.: 32422 Cov.: 32 AF XY: 0.613 AC XY: 45578 AN XY: 74362

African (AFR) AF: 0.211 AC: 8757 AN: 41506

American (AMR) AF: 0.621 AC: 9482 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2509 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3948 AN: 5158

South Asian (SAS) AF: 0.840 AC: 4052 AN: 4822

European-Finnish (FIN) AF: 0.821 AC: 8704 AN: 10596

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52310 AN: 67982

Other (OTH) AF: 0.613 AC: 1294 AN: 2112

Alfa AF: 0.711 Hom.: 125643

Bravo AF: 0.566

Asia WGS AF: 0.767 AC: 2665 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	6.7
DANN	Benign	0.63
PhyloP100		-0.089
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: rs7572473; hg19: chr2-200634917;