9-61192779-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_015667.2(SPATA31A7):​c.693C>A​(p.Asp231Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0052 ( 4 hom., cov: 5)
Exomes 𝑓: 0.0077 ( 399 hom. )
Failed GnomAD Quality Control

Consequence

SPATA31A7
NM_015667.2 missense

Scores

7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.193
Variant links:
Genes affected
SPATA31A7 (HGNC:32007): (SPATA31 subfamily A member 7) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.008272499).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPATA31A7NM_015667.2 linkc.693C>A p.Asp231Glu missense_variant Exon 4 of 4 ENST00000619167.2 NP_056482.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPATA31A7ENST00000619167.2 linkc.693C>A p.Asp231Glu missense_variant Exon 4 of 4 1 NM_015667.2 ENSP00000484807.1 Q8IWB4

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
143
AN:
27222
Hom.:
4
Cov.:
5
FAILED QC
Gnomad AFR
AF:
0.00161
Gnomad AMI
AF:
0.0149
Gnomad AMR
AF:
0.00206
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00163
Gnomad FIN
AF:
0.00716
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00837
Gnomad OTH
AF:
0.00243
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00773
AC:
4785
AN:
618772
Hom.:
399
Cov.:
8
AF XY:
0.00747
AC XY:
2376
AN XY:
318196
show subpopulations
Gnomad4 AFR exome
AF:
0.00123
Gnomad4 AMR exome
AF:
0.00340
Gnomad4 ASJ exome
AF:
0.000253
Gnomad4 EAS exome
AF:
0.0000325
Gnomad4 SAS exome
AF:
0.000734
Gnomad4 FIN exome
AF:
0.00829
Gnomad4 NFE exome
AF:
0.0100
Gnomad4 OTH exome
AF:
0.00606
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00525
AC:
143
AN:
27244
Hom.:
4
Cov.:
5
AF XY:
0.00489
AC XY:
60
AN XY:
12272
show subpopulations
Gnomad4 AFR
AF:
0.00161
Gnomad4 AMR
AF:
0.00205
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00164
Gnomad4 FIN
AF:
0.00716
Gnomad4 NFE
AF:
0.00837
Gnomad4 OTH
AF:
0.00242
Alfa
AF:
0.000938
Hom.:
0

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Sep 18, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.693C>A (p.D231E) alteration is located in exon 4 (coding exon 4) of the SPATA31A7 gene. This alteration results from a C to A substitution at nucleotide position 693, causing the aspartic acid (D) at amino acid position 231 to be replaced by a glutamic acid (E). 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
0.19
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.69
DANN
Benign
0.49
DEOGEN2
Benign
0.031
T
LIST_S2
Benign
0.42
T
MetaRNN
Benign
0.0083
T
Sift4G
Benign
0.35
T
Vest4
0.037
gMVP
0.036

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: rs1264650231; hg19: chr9-43627994; API