chr3-197773479-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_032288.7(FYTTD1):​c.574C>G​(p.Leu192Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,440,550 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L192F) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

FYTTD1
NM_032288.7 missense

Scores

1
9
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.49
Variant links:
Genes affected
FYTTD1 (HGNC:25407): (forty-two-three domain containing 1) Enables mRNA binding activity. Involved in mRNA export from nucleus. Located in nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FYTTD1NM_032288.7 linkc.574C>G p.Leu192Val missense_variant Exon 5 of 9 ENST00000241502.9 NP_115664.2 Q96QD9-1A0A024R9K4
FYTTD1NM_001011537.3 linkc.496C>G p.Leu166Val missense_variant Exon 6 of 10 NP_001011537.2 Q96QD9-2
FYTTD1NR_027840.2 linkn.1047C>G non_coding_transcript_exon_variant Exon 5 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FYTTD1ENST00000241502.9 linkc.574C>G p.Leu192Val missense_variant Exon 5 of 9 1 NM_032288.7 ENSP00000241502.3 Q96QD9-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.94e-7
AC:
1
AN:
1440550
Hom.:
0
Cov.:
27
AF XY:
0.00000140
AC XY:
1
AN XY:
716034
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000119
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.70
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Uncertain
-0.070
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.047
.;.;T;.
Eigen
Uncertain
0.27
Eigen_PC
Uncertain
0.37
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Uncertain
0.91
D;D;D;D
M_CAP
Benign
0.012
T
MetaRNN
Uncertain
0.62
D;D;D;D
MetaSVM
Benign
-0.64
T
MutationAssessor
Benign
1.5
.;.;L;.
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-1.9
N;N;N;N
REVEL
Benign
0.21
Sift
Benign
0.047
D;D;D;D
Sift4G
Benign
0.16
T;T;T;T
Polyphen
1.0, 0.0060
.;D;B;.
Vest4
0.42, 0.43, 0.42
MutPred
0.74
.;.;Gain of sheet (P = 0.0344);.;
MVP
0.21
MPC
0.19
ClinPred
0.85
D
GERP RS
5.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.25
gMVP
0.30

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-197500350; API