3-184344876-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_144635.5(FAM131A):​c.1007C>T​(p.Thr336Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000399 in 1,610,876 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00067 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00037 ( 1 hom. )

Consequence

FAM131A
NM_144635.5 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -3.73
Variant links:
Genes affected
FAM131A (HGNC:28308): (family with sequence similarity 131 member A)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.00475353).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM131ANM_144635.5 linkuse as main transcriptc.1007C>T p.Thr336Met missense_variant 6/6 ENST00000383847.7 NP_653236.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM131AENST00000383847.7 linkuse as main transcriptc.1007C>T p.Thr336Met missense_variant 6/62 NM_144635.5 ENSP00000373360 A1Q6UXB0-3

Frequencies

GnomAD3 genomes
AF:
0.000670
AC:
102
AN:
152216
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000772
Gnomad AMI
AF:
0.0231
Gnomad AMR
AF:
0.000785
Gnomad ASJ
AF:
0.00288
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000368
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.000383
AC:
94
AN:
245142
Hom.:
0
AF XY:
0.000427
AC XY:
57
AN XY:
133538
show subpopulations
Gnomad AFR exome
AF:
0.000831
Gnomad AMR exome
AF:
0.000261
Gnomad ASJ exome
AF:
0.00261
Gnomad EAS exome
AF:
0.0000548
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000527
Gnomad NFE exome
AF:
0.000395
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000370
AC:
540
AN:
1458542
Hom.:
1
Cov.:
32
AF XY:
0.000383
AC XY:
278
AN XY:
725774
show subpopulations
Gnomad4 AFR exome
AF:
0.000329
Gnomad4 AMR exome
AF:
0.000268
Gnomad4 ASJ exome
AF:
0.00207
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.0000199
Gnomad4 NFE exome
AF:
0.000392
Gnomad4 OTH exome
AF:
0.000365
GnomAD4 genome
AF:
0.000670
AC:
102
AN:
152334
Hom.:
0
Cov.:
33
AF XY:
0.000618
AC XY:
46
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.000769
Gnomad4 AMR
AF:
0.000784
Gnomad4 ASJ
AF:
0.00288
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000368
Gnomad4 OTH
AF:
0.000474
Alfa
AF:
0.000584
Hom.:
0
Bravo
AF:
0.000808
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00114
AC:
5
ESP6500EA
AF:
0.000349
AC:
3
ExAC
AF:
0.000313
AC:
38
EpiCase
AF:
0.000545
EpiControl
AF:
0.000890

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 GeneticsDec 14, 2022The c.1007C>T (p.T336M) alteration is located in exon 6 (coding exon 6) of the FAM131A gene. This alteration results from a C to T substitution at nucleotide position 1007, causing the threonine (T) at amino acid position 336 to be replaced by a methionine (M). 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
AlphaMissense
Benign
0.073
BayesDel_addAF
Benign
-0.67
T
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.0070
DANN
Benign
0.90
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.021
N
LIST_S2
Benign
0.25
.;.;T;T;T;T
M_CAP
Benign
0.0074
T
MetaRNN
Benign
0.0048
T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
.;.;.;.;.;N
MutationTaster
Benign
1.0
N;N;N;N;N;N;N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-0.20
N;N;.;N;N;N
REVEL
Benign
0.0050
Sift
Benign
0.74
T;T;.;T;T;T
Sift4G
Benign
0.11
T;T;.;T;T;T
Vest4
0.10
MVP
0.085
MPC
0.41
ClinPred
0.0069
T
GERP RS
-4.6
Varity_R
0.053
gMVP
0.24

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: rs144826588; hg19: chr3-184062664; COSMIC: COSV55599227; COSMIC: COSV55599227; API