rs7605378

Variant names:

• chr2-199812203-A-C
• rs7605378
• NM_001363886.2:c.*502T>G

Variant summary

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

The NM_001363886.2(FTCDNL1):​c.*502T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,950 control chromosomes in the GnomAD database, including 31,231 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 0.64 (31231 hom., cov: 31)
• Consequence: FTCDNL1 NM_001363886.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 22 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 (SAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FTCDNL1	NM_001363886.2	c.*502T>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000420128.6	NP_001350815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000420128.6	c.*502T>G		3_prime_UTR_variant	Exon 5 of 5	5	NM_001363886.2	ENSP00000457780.1
FTCDNL1	ENST00000416668.5	c.211+33872T>G		intron_variant	Intron 3 of 3	1		ENSP00000454447.1
FTCDNL1	ENST00000420922.6	c.*19+32177T>G		intron_variant	Intron 4 of 4	5		ENSP00000456442.1
FTCDNL1	ENST00000642693.1	n.405+7369T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96978 AN: 151832 Hom.: 31222 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.639 AC: 97030 AN: 151950 Hom.: 31231 Cov.: 31 AF XY: 0.637 AC XY: 47302 AN XY: 74286

African (AFR) AF: 0.579 AC: 23971 AN: 41400

American (AMR) AF: 0.602 AC: 9199 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2595 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2712 AN: 5152

South Asian (SAS) AF: 0.767 AC: 3690 AN: 4812

European-Finnish (FIN) AF: 0.580 AC: 6127 AN: 10564

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46516 AN: 67968

Other (OTH) AF: 0.639 AC: 1349 AN: 2110

Alfa AF: 0.672 Hom.: 123272

Bravo AF: 0.633

Asia WGS AF: 0.636 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs7605378; hg19: chr2-200676926;