9-61192779-C-A

Variant names:

• chr9-61192779-C-A
• rs1264650231
• NM_015667.2:c.693C>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
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.193

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]

ACMG classification

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
SPATA31A7	NM_015667.2	c.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
SPATA31A7	ENST00000619167.2	c.693C>A	p.Asp231Glu	missense_variant	Exon 4 of 4	1	NM_015667.2	ENSP00000484807.1

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

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

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

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

Other links and lift over

dbSNP: rs1264650231; hg19: chr9-43627994;