rs7605378

chr2-199812203-A-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• 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/exons	MANE	UniProt
FTCDNL1	NM_001363886.2	c.*502T>G		3_prime_UTR_variant	5/5	ENST00000420128.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FTCDNL1	ENST00000420128.6	c.*502T>G		3_prime_UTR_variant	5/5	5	NM_001363886.2
FTCDNL1	ENST00000416668.5	c.211+33872T>G		intron_variant		1
FTCDNL1	ENST00000420922.6	c.*19+32177T>G		intron_variant		5		P1
FTCDNL1	ENST00000642693.1	n.405+7369T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.639

Alfa AF: 0.679 Hom.: 58757

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7605378; hg19: chr2-200676926;