chr4-151566353-C-T

Variant summary

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

The NM_001109977.3(FHIP1A):​c.94C>T​(p.His32Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000718 in 1,392,998 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

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

Consequence

FHIP1A
NM_001109977.3 missense

Scores

7
8
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.11
Variant links:
Genes affected
FHIP1A (HGNC:34237): (FHF complex subunit HOOK interacting protein 1A) Involved in protein localization to perinuclear region of cytoplasm. [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
FHIP1ANM_001109977.3 linkc.94C>T p.His32Tyr missense_variant Exon 4 of 14 ENST00000435205.6 NP_001103447.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FHIP1AENST00000435205.6 linkc.94C>T p.His32Tyr missense_variant Exon 4 of 14 5 NM_001109977.3 ENSP00000413196.1 Q05DH4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.18e-7
AC:
1
AN:
1392998
Hom.:
0
Cov.:
27
AF XY:
0.00000145
AC XY:
1
AN XY:
687500
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:
0.0000126
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000301
Hom.:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 08, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.94C>T (p.H32Y) alteration is located in exon 4 (coding exon 1) of the FAM160A1 gene. This alteration results from a C to T substitution at nucleotide position 94, causing the histidine (H) at amino acid position 32 to be replaced by a tyrosine (Y). 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
Pathogenic
0.95
BayesDel_addAF
Pathogenic
0.24
D
BayesDel_noAF
Uncertain
0.10
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.15
.;T;T;.;T
Eigen
Pathogenic
0.79
Eigen_PC
Pathogenic
0.78
FATHMM_MKL
Uncertain
0.83
D
LIST_S2
Uncertain
0.94
D;D;D;D;.
M_CAP
Benign
0.018
T
MetaRNN
Uncertain
0.67
D;D;D;D;D
MetaSVM
Benign
-0.84
T
MutationAssessor
Uncertain
2.5
.;M;.;.;M
PrimateAI
Uncertain
0.73
T
PROVEAN
Pathogenic
-6.0
D;D;D;D;D
REVEL
Uncertain
0.36
Sift
Pathogenic
0.0
D;D;D;D;D
Sift4G
Pathogenic
0.0
D;D;D;D;D
Polyphen
1.0
.;D;.;.;D
Vest4
0.72, 0.71
MutPred
0.68
Loss of ubiquitination at K30 (P = 0.1202);Loss of ubiquitination at K30 (P = 0.1202);Loss of ubiquitination at K30 (P = 0.1202);Loss of ubiquitination at K30 (P = 0.1202);Loss of ubiquitination at K30 (P = 0.1202);
MVP
0.17
ClinPred
0.99
D
GERP RS
5.9
Varity_R
0.82
gMVP
0.84

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: rs1415904460; hg19: chr4-152487505; API