NM_001174072.3:c.1348G>T

Variant summary

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

The NM_001174072.3(SERINC5):​c.1348G>T​(p.Ala450Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000723 in 1,383,818 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. A450T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

SERINC5
NM_001174072.3 missense

Scores

8
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.01
Variant links:
Genes affected
SERINC5 (HGNC:18825): (serine incorporator 5) Predicted to enable L-serine transmembrane transporter activity. Involved in defense response to virus; detection of virus; and innate immune response. Located in several cellular components, including centrosome; cytosol; and plasma membrane. [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
SERINC5NM_001174072.3 linkc.1348G>T p.Ala450Ser missense_variant Exon 12 of 12 ENST00000507668.7 NP_001167543.1 Q86VE9-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SERINC5ENST00000507668.7 linkc.1348G>T p.Ala450Ser missense_variant Exon 12 of 12 2 NM_001174072.3 ENSP00000426237.3 Q86VE9-4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000746
AC:
1
AN:
134088
Hom.:
0
AF XY:
0.0000137
AC XY:
1
AN XY:
72980
show subpopulations
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 SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000191
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
7.23e-7
AC:
1
AN:
1383818
Hom.:
0
Cov.:
34
AF XY:
0.00000146
AC XY:
1
AN XY:
682852
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:
9.27e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
0.0
CADD
Benign
22
DANN
Uncertain
1.0
Eigen
Uncertain
0.25
Eigen_PC
Benign
0.18
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.87
D
M_CAP
Benign
0.068
D
MetaRNN
Uncertain
0.43
T
MetaSVM
Benign
-0.70
T
PrimateAI
Uncertain
0.51
T
Sift4G
Benign
0.061
T
Vest4
0.43
MVP
0.23
ClinPred
0.89
D
GERP RS
4.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
gMVP
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.15
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: rs537411704; hg19: chr5-79439524; API