9-61192717-C-T

Variant names:

• chr9-61192717-C-T
• rs1176047740
• NM_015667.2:c.631C>T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_015667.2(SPATA31A7):​c.631C>T​(p.Pro211Ser) 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 Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0075 (0 hom., cov: 6)
  • Exomes 𝑓: 0.0086 (144 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31A7 NM_015667.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.469

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 -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.008683622).
• BP6: Variant 9-61192717-C-T is Benign according to our data. Variant chr9-61192717-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2205976.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31A7	NM_015667.2	c.631C>T	p.Pro211Ser	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.631C>T	p.Pro211Ser	missense_variant	Exon 4 of 4	1	NM_015667.2	ENSP00000484807.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 296 AN: 39514 Hom.: 0 Cov.: 6 FAILED QC

Gnomad AFR AF: 0.00141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00476

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00294

Gnomad FIN AF: 0.0117

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.00196

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00864 AC: 7920 AN: 916536 Hom.: 144 Cov.: 13 AF XY: 0.00856 AC XY: 3969 AN XY: 463594

Gnomad4 AFR exome AF: 0.00165

Gnomad4 AMR exome AF: 0.00301

Gnomad4 ASJ exome AF: 0.00158

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00136

Gnomad4 FIN exome AF: 0.0121

Gnomad4 NFE exome AF: 0.0104

Gnomad4 OTH exome AF: 0.00652

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00746 AC: 295 AN: 39568 Hom.: 0 Cov.: 6 AF XY: 0.00702 AC XY: 128 AN XY: 18244

Gnomad4 AFR AF: 0.00140

Gnomad4 AMR AF: 0.00475

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00147

Gnomad4 FIN AF: 0.0117

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.00195

Alfa AF: 0.00649 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 23, 2022

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.085
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.40
DEOGEN2	Benign	0.031	T
LIST_S2	Benign	0.48	T
MetaRNN	Benign	0.0087	T
Sift4G	Benign	0.12	T
Vest4		0.054
gMVP		0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1176047740; hg19: chr9-43628056;