chr2-199804385-G-A

Variant names:

• chr2-199804385-G-A
• rs4673491
• ENST00000416668.5:c.211+41690C>T

Variant summary

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

The ENST00000416668.5(FTCDNL1):​c.211+41690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,158 control chromosomes in the GnomAD database, including 1,439 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 0.12 (1439 hom., cov: 32)
• Consequence: FTCDNL1 ENST00000416668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416668.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	NM_001350854.2		c.*19+39995C>T		intron	N/A	NP_001337783.1
	FTCDNL1	NM_001350855.2		c.211+41690C>T		intron	N/A	NP_001337784.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	ENST00000416668.5	TSL:1	c.211+41690C>T		intron	N/A	ENSP00000454447.1
	FTCDNL1	ENST00000420922.6	TSL:5	c.*19+39995C>T		intron	N/A	ENSP00000456442.1
	FTCDNL1	ENST00000642693.1		n.405+15187C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17946 AN: 152040 Hom.: 1439 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.0825

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.118 AC: 17942 AN: 152158 Hom.: 1439 Cov.: 32 AF XY: 0.121 AC XY: 9034 AN XY: 74364

African (AFR) AF: 0.0286 AC: 1189 AN: 41536

American (AMR) AF: 0.0778 AC: 1191 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3472

East Asian (EAS) AF: 0.0827 AC: 428 AN: 5174

South Asian (SAS) AF: 0.0717 AC: 345 AN: 4812

European-Finnish (FIN) AF: 0.291 AC: 3070 AN: 10544

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11032 AN: 68006

Other (OTH) AF: 0.107 AC: 225 AN: 2108

Alfa AF: 0.137 Hom.: 631

Bravo AF: 0.0988

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.82
PhyloP100		0.053
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: rs4673491; hg19: chr2-200669108;