rs1260243604

Variant summary

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

The NM_001137548.3(FAM25C):​c.263G>T​(p.Gly88Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000135 in 148,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/15 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. G88E) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 29)
Exomes 𝑓: 7.3e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FAM25C
NM_001137548.3 missense

Scores

1
1
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.64
Variant links:
Genes affected
FAM25C (HGNC:23586): (family with sequence similarity 25 member C)

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=0.14891914).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM25CNM_001137548.3 linkc.263G>T p.Gly88Val missense_variant Exon 3 of 3 ENST00000617224.3 NP_001131020.1 B3EWG3B3EWG5B3EWG6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM25CENST00000617224.3 linkc.263G>T p.Gly88Val missense_variant Exon 3 of 3 1 NM_001137548.3 ENSP00000485370.1 B3EWG5

Frequencies

GnomAD3 genomes
AF:
0.0000135
AC:
2
AN:
148016
Hom.:
0
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0000497
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000697
AC:
1
AN:
143374
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
76524
show subpopulations
Gnomad AFR exome
AF:
0.000131
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
7.32e-7
AC:
1
AN:
1366624
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
675024
show subpopulations
Gnomad4 AFR exome
AF:
0.0000320
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000135
AC:
2
AN:
148016
Hom.:
0
Cov.:
29
AF XY:
0.0000139
AC XY:
1
AN XY:
71986
show subpopulations
Gnomad4 AFR
AF:
0.0000497
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
22
DANN
Benign
0.74
DEOGEN2
Benign
0.098
T
Eigen
Benign
-0.61
Eigen_PC
Benign
-0.81
FATHMM_MKL
Benign
0.019
N
M_CAP
Benign
0.00081
T
MetaRNN
Benign
0.15
T
MetaSVM
Benign
-1.0
T
PrimateAI
Uncertain
0.51
T
Sift4G
Pathogenic
0.0
D
Vest4
0.42
MVP
0.30
ClinPred
0.14
T
GERP RS
0.35
Varity_R
0.27
gMVP
0.014

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: rs1260243604; hg19: chr10-49203418; API