rs7572473

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000416668.5(FTCDNL1):​c.212-9359G>T variant causes a intron 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
ENST00000416668.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0890
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
FTCDNL1NM_001350854.2 linkuse as main transcriptc.*20-9359G>T intron_variant
FTCDNL1NM_001350855.2 linkuse as main transcriptc.212-9359G>T intron_variant
FTCDNL1XM_024452852.2 linkuse as main transcriptc.397+49378G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FTCDNL1ENST00000416668.5 linkuse as main transcriptc.212-9359G>T intron_variant 1
FTCDNL1ENST00000420922.6 linkuse as main transcriptc.*20-9359G>T intron_variant 5 P1

Frequencies

GnomAD3 genomes
AF:
0.605
AC:
91921
AN:
152004
Hom.:
32426
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.211
Gnomad4 AMR
AF:
0.621
Gnomad4 ASJ
AF:
0.723
Gnomad4 EAS
AF:
0.765
Gnomad4 SAS
AF:
0.840
Gnomad4 FIN
AF:
0.821
Gnomad4 NFE
AF:
0.769
Gnomad4 OTH
AF:
0.613
Alfa
AF:
0.735
Hom.:
92080
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

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.

Other links and lift over

dbSNP: rs7572473; hg19: chr2-200634917; API