dbSNP rs6759644: FTCDNL1:c.212-30663A>G (chr2-199791498-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001350854.2(FTCDNL1):c.*20-30663A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,918 control chromosomes in the GnomAD database, including 26,014 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 0.58 ( 26014 hom., cov: 32)

Consequence

FTCDNL1
NM_001350854.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Variant links:

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]

FTCDNL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
FTCDNL1	XM_024452854.2 link	c.*4234A>G	3_prime_UTR_variant	Exon 5 of 5	XP_024308622.1
FTCDNL1	NM_001350854.2 link	c.*20-30663A>G	intron_variant	Intron 4 of 4	NP_001337783.1
FTCDNL1	NM_001350855.2 link	c.212-30663A>G	intron_variant	Intron 3 of 3	NP_001337784.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
FTCDNL1	ENST00000416668.5 link	c.212-30663A>G	intron_variant	Intron 3 of 3	1	ENSP00000454447.1	H3BMM2
FTCDNL1	ENST00000420922.6 link	c.*20-30663A>G	intron_variant	Intron 4 of 4	5	ENSP00000456442.1	H3BRX2
FTCDNL1	ENST00000642693.1 link	n.406-5920A>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

87511

AN:

151800

Hom.:

25985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.842

Gnomad SAS

AF:

0.613

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.592

Gnomad OTH

AF:

0.534

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

GnomAD4 genome

AF:

0.577

AC:

87589

AN:

151918

Hom.:

26014

Cov.:

AF XY:

0.585

AC XY:

43432

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.470

Gnomad4 AMR

AF:

0.657

Gnomad4 ASJ

AF:

0.504

Gnomad4 EAS

AF:

0.843

Gnomad4 SAS

AF:

0.613

Gnomad4 FIN

AF:

0.686

Gnomad4 NFE

AF:

0.592

Gnomad4 OTH

AF:

0.540

Alfa

AF:

0.539

Hom.:

2463

Bravo

AF:

0.568

Asia WGS

AF:

0.737

AC:

2557

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.71

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over