9-42185736-C-T

Variant summary

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

The NM_001145196.1(SPATA31A6):​c.289C>T​(p.Leu97Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 1,140,742 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 20)
Exomes 𝑓: 0.0000044 ( 1 hom. )

Consequence

SPATA31A6
NM_001145196.1 missense

Scores

1
1
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.854
Variant links:
Genes affected
SPATA31A6 (HGNC:32006): (SPATA31 subfamily A member 6) Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle. [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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16399667).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPATA31A6NM_001145196.1 linkc.289C>T p.Leu97Phe missense_variant Exon 3 of 4 ENST00000332857.7 NP_001138668.1 Q5VVP1
SPATA31A6XM_011517871.4 linkc.325C>T p.Leu109Phe missense_variant Exon 3 of 4 XP_011516173.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPATA31A6ENST00000332857.7 linkc.289C>T p.Leu97Phe missense_variant Exon 3 of 4 1 NM_001145196.1 ENSP00000329825.6 Q5VVP1
SPATA31A6ENST00000496386.1 linkn.140C>T non_coding_transcript_exon_variant Exon 2 of 3 5

Frequencies

GnomAD3 genomes
Cov.:
20
GnomAD4 exome
AF:
0.00000438
AC:
5
AN:
1140742
Hom.:
1
Cov.:
32
AF XY:
0.00000350
AC XY:
2
AN XY:
571934
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:
0.00000584
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
20

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Feb 27, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.289C>T (p.L97F) alteration is located in exon 3 (coding exon 3) of the SPATA31A6 gene. This alteration results from a C to T substitution at nucleotide position 289, causing the leucine (L) at amino acid position 97 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
0.18
CADD
Benign
15
DEOGEN2
Benign
0.099
T
LIST_S2
Benign
0.54
T
MetaRNN
Benign
0.16
T
PROVEAN
Benign
-1.6
N
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.0030
D
Vest4
0.30
gMVP
0.11

Splicing

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: rs1174262649; hg19: -; API