3-197768532-C-A

Variant names:

• chr3-197768532-C-A
• rs767355362
• NM_032288.7:c.329C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032288.7(FYTTD1):​c.329C>A​(p.Thr110Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. 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. T110M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FYTTD1 NM_032288.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.54
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21030256).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032288.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYTTD1	NM_032288.7	MANE Select	c.329C>A	p.Thr110Lys	missense	Exon 3 of 9	NP_115664.2
	FYTTD1	NM_001011537.3		c.251C>A	p.Thr84Lys	missense	Exon 4 of 10	NP_001011537.2	Q96QD9-2
	FYTTD1	NR_027840.2		n.802C>A		non_coding_transcript_exon	Exon 3 of 9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYTTD1	ENST00000241502.9	TSL:1 MANE Select	c.329C>A	p.Thr110Lys	missense	Exon 3 of 9	ENSP00000241502.3	Q96QD9-1
	FYTTD1	ENST00000966386.1		c.329C>A	p.Thr110Lys	missense	Exon 3 of 10	ENSP00000636445.1
	FYTTD1	ENST00000966385.1		c.329C>A	p.Thr110Lys	missense	Exon 3 of 9	ENSP00000636444.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251354 AF XY: 0.00000736

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.026	T
Eigen	Benign	-0.045
Eigen_PC	Benign	0.16
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.79	T
M_CAP	Benign	0.0071	T
MetaRNN	Benign	0.21	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PhyloP100		3.5
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.046
Sift	Benign	0.051	T
Sift4G	Benign	0.13	T
Polyphen		0.065	B
Vest4		0.44
MutPred		0.45		Loss of phosphorylation at T110 (P = 0.0716)
MVP		0.043
MPC		0.27
ClinPred		0.67	D
GERP RS		5.2
Varity_R		0.19
gMVP		0.38
Mutation Taster		=93/7	polymorphism

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

Other links and lift over

dbSNP: rs767355362; hg19: chr3-197495403;