rs10113875

Variant summary

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

The NM_002171.2(IFNA10):​c.97G>T​(p.Gly33Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,611,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000027 ( 0 hom. )

Consequence

IFNA10
NM_002171.2 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14
Variant links:
Genes affected
IFNA10 (HGNC:5418): (interferon alpha 10) This gene encodes a protein that belongs to the type I interferon family of proteins, and is located in a cluster of alpha interferon genes on chromosome 9. Interferons are small regulatory molecules that function in cell signaling in response to viruses and other pathogens or tumor cells. This gene is intronless and the encoded protein is secreted. [provided by RefSeq, Aug 2013]

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=0.05607906).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IFNA10NM_002171.2 linkc.97G>T p.Gly33Cys missense_variant Exon 1 of 1 ENST00000357374.2 NP_002162.1 P01566A0A7R8C2Z1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IFNA10ENST00000357374.2 linkc.97G>T p.Gly33Cys missense_variant Exon 1 of 1 6 NM_002171.2 ENSP00000369566.1 P01566

Frequencies

GnomAD3 genomes
AF:
0.000225
AC:
34
AN:
151378
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000757
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000657
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:
0.000957
GnomAD3 exomes
AF:
0.0000764
AC:
18
AN:
235466
Hom.:
0
AF XY:
0.0000629
AC XY:
8
AN XY:
127242
show subpopulations
Gnomad AFR exome
AF:
0.00109
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000563
Gnomad SAS exome
AF:
0.0000345
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000267
AC:
39
AN:
1460402
Hom.:
0
Cov.:
33
AF XY:
0.0000275
AC XY:
20
AN XY:
726532
show subpopulations
Gnomad4 AFR exome
AF:
0.000571
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000117
Gnomad4 OTH exome
AF:
0.0000497
GnomAD4 genome
AF:
0.000224
AC:
34
AN:
151498
Hom.:
0
Cov.:
31
AF XY:
0.000351
AC XY:
26
AN XY:
74040
show subpopulations
Gnomad4 AFR
AF:
0.000754
Gnomad4 AMR
AF:
0.0000656
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:
0.000947
ExAC
AF:
0.0000824
AC:
10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.57
T
BayesDel_noAF
Benign
-0.68
CADD
Benign
0.065
DANN
Benign
0.97
DEOGEN2
Benign
0.0022
T
Eigen
Benign
-0.74
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.012
N
LIST_S2
Benign
0.67
T
M_CAP
Benign
0.0055
T
MetaRNN
Benign
0.056
T
MetaSVM
Benign
-0.96
T
MutationAssessor
Uncertain
2.5
M
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-2.1
N
REVEL
Benign
0.046
Sift
Benign
0.19
T
Sift4G
Uncertain
0.052
T
Polyphen
0.99
D
Vest4
0.076
MVP
0.44
MPC
0.42
ClinPred
0.091
T
GERP RS
-4.7
Varity_R
0.16
gMVP
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs10113875; hg19: chr9-21207000; COSMIC: COSV53330735; COSMIC: COSV53330735; API