5-132814114-C-T

Variant summary

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

The NM_175873.6(SOWAHA):​c.493C>T​(p.Leu165Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,446,378 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SOWAHA
NM_175873.6 missense

Scores

1
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0350
Variant links:
Genes affected
SOWAHA (HGNC:27033): (sosondowah ankyrin repeat domain family member A)

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=0.07620266).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SOWAHANM_175873.6 linkc.493C>T p.Leu165Phe missense_variant Exon 1 of 1 ENST00000378693.4 NP_787069.4 Q2M3V2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SOWAHAENST00000378693.4 linkc.493C>T p.Leu165Phe missense_variant Exon 1 of 1 6 NM_175873.6 ENSP00000367965.2 Q2M3V2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000917
AC:
2
AN:
218210
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
121876
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000115
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:
0.00000138
AC:
2
AN:
1446378
Hom.:
0
Cov.:
38
AF XY:
0.00000139
AC XY:
1
AN XY:
719772
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000505
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.:
33
ExAC
AF:
0.00000871
AC:
1

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Feb 05, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.493C>T (p.L165F) alteration is located in exon 1 (coding exon 1) of the SOWAHA gene. This alteration results from a C to T substitution at nucleotide position 493, causing the leucine (L) at amino acid position 165 to be replaced by a phenylalanine (F). 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
Benign
0.11
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
4.7
DANN
Benign
0.89
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.041
N
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.076
T
MetaSVM
Benign
-1.0
T
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-1.1
N
REVEL
Benign
0.015
Sift
Benign
0.085
T
Sift4G
Benign
0.59
T
Vest4
0.052
MutPred
0.26
Loss of glycosylation at P166 (P = 0.2049);
MVP
0.030
ClinPred
0.057
T
GERP RS
-4.4
gMVP
0.23

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: rs774676243; hg19: chr5-132149806; API