3-56633068-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001365635.2(TASOR):​c.3723G>T​(p.Glu1241Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000069 in 1,449,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000069 ( 0 hom. )

Consequence

TASOR
NM_001365635.2 missense

Scores

5
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.346
Variant links:
Genes affected
TASOR (HGNC:30314): (transcription activation suppressor) Enables chromatin binding activity. Involved in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate; protein localization to heterochromatin; and regulation of gene expression. Located in heterochromatin and nucleoplasm. [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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1577141).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TASORNM_001365635.2 linkuse as main transcriptc.3723G>T p.Glu1241Asp missense_variant 18/24 ENST00000683822.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TASORENST00000683822.1 linkuse as main transcriptc.3723G>T p.Glu1241Asp missense_variant 18/24 NM_001365635.2 A2Q9UK61-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000690
AC:
10
AN:
1449326
Hom.:
0
Cov.:
30
AF XY:
0.00000972
AC XY:
7
AN XY:
720506
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000903
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 26, 2024The c.3723G>T (p.E1241D) alteration is located in exon 18 (coding exon 18) of the FAM208A gene. This alteration results from a G to T substitution at nucleotide position 3723, causing the glutamic acid (E) at amino acid position 1241 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.037
.;.;.;T
Eigen
Benign
0.11
Eigen_PC
Benign
0.096
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Uncertain
0.87
D;D;D;D
M_CAP
Benign
0.0087
T
MetaRNN
Benign
0.16
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
0.97
D;D;D
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
0.47
N;N;N;.
REVEL
Benign
0.087
Sift
Benign
0.21
T;T;.;.
Sift4G
Uncertain
0.018
D;D;D;D
Polyphen
1.0
D;D;P;.
Vest4
0.43
MutPred
0.20
.;Loss of disorder (P = 0.1184);.;.;
MVP
0.38
MPC
0.81
ClinPred
0.75
D
GERP RS
1.3
gMVP
0.11

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs745872840; hg19: chr3-56667096; API