rs746490997

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_032727.4(INA):​c.157G>A​(p.Ala53Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,414,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

INA
NM_032727.4 missense

Scores

1
2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.171
Variant links:
Genes affected
INA (HGNC:6057): (internexin neuronal intermediate filament protein alpha) Neurofilaments are type IV intermediate filament heteropolymers composed of light, medium, and heavy chains. Neurofilaments comprise the axoskeleton and they functionally maintain the neuronal caliber. They may also play a role in intracellular transport to axons and dendrites. This gene is a member of the intermediate filament family and is involved in the morphogenesis of neurons. [provided by RefSeq, Jun 2009]
NT5C2 (HGNC:8022): (5'-nucleotidase, cytosolic II) This gene encodes a hydrolase that serves as an important role in cellular purine metabolism by acting primarily on inosine 5'-monophosphate and other purine nucleotides. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2948119).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
INANM_032727.4 linkc.157G>A p.Ala53Thr missense_variant Exon 1 of 3 ENST00000369849.9 NP_116116.1 Q16352

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
INAENST00000369849.9 linkc.157G>A p.Ala53Thr missense_variant Exon 1 of 3 1 NM_032727.4 ENSP00000358865.4 Q16352
NT5C2ENST00000676449.1 linkc.-239C>T 5_prime_UTR_variant Exon 1 of 18 ENSP00000502801.1 P49902-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000111
AC:
2
AN:
179728
Hom.:
0
AF XY:
0.00000985
AC XY:
1
AN XY:
101538
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000713
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
AF:
0.00000141
AC:
2
AN:
1414418
Hom.:
0
Cov.:
32
AF XY:
0.00000142
AC XY:
1
AN XY:
702596
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000500
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
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.29
CADD
Benign
18
DANN
Uncertain
1.0
DEOGEN2
Benign
0.31
T
Eigen
Benign
-0.35
Eigen_PC
Benign
-0.38
FATHMM_MKL
Benign
0.051
N
LIST_S2
Benign
0.60
T
M_CAP
Pathogenic
0.88
D
MetaRNN
Benign
0.29
T
MetaSVM
Benign
-0.62
T
MutationAssessor
Benign
0.81
L
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
0.10
N
REVEL
Benign
0.21
Sift
Benign
0.32
T
Sift4G
Benign
0.57
T
Polyphen
0.85
P
Vest4
0.12
MutPred
0.37
Gain of glycosylation at A53 (P = 0.0072);
MVP
0.88
MPC
1.0
ClinPred
0.19
T
GERP RS
1.7
Varity_R
0.039
gMVP
0.48

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: rs746490997; hg19: chr10-105037125; COSMIC: COSV63975722; API