Genetic Variant SPATA31C2:p.Ser1105del (chr9-88129719-TCTG-T) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2

The NM_001350978.3(SPATA31C2):c.3315_3317delCAG(p.Ser1105del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 1,603,086 control chromosomes in the GnomAD database, including 47 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 4 hom., cov: 28)

Exomes 𝑓: 0.0035 ( 43 hom. )

Consequence

SPATA31C2
NM_001350978.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0120

Variant links:

Genes affected

SPATA31C2 (HGNC:24508): (SPATA31 subfamily C member 2) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA31C2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001350978.3. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 9-88129719-TCTG-T is Benign according to our data. Variant chr9-88129719-TCTG-T is described in ClinVar as [Likely_benign]. Clinvar id is 3898068.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31C2	NM_001350978.3 link	c.3315_3317delCAG	p.Ser1105del	disruptive_inframe_deletion	Exon 4 of 4	ENST00000324915.6	NP_001337907.1
SPATA31C2	NM_001166137.1 link	c.3315_3317delCAG	p.Ser1105del	disruptive_inframe_deletion	Exon 4 of 4		NP_001159609.1	B4DYI2Q9Y4N5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31C2	ENST00000324915.6 link	c.3315_3317delCAG	p.Ser1105del	disruptive_inframe_deletion	Exon 4 of 4	6	NM_001350978.3	ENSP00000509734.1		A0A8I5KWQ5
SPATA31C2	ENST00000675441.1 link	c.3315_3317delCAG	p.Ser1105del	disruptive_inframe_deletion	Exon 4 of 4			ENSP00000509164.1		B4DYI2

Frequencies

GnomAD3 genomes

AF:

0.00332

AC:

505

AN:

151918

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00297

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000416

Gnomad FIN

AF:

0.0146

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00375

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00363

AC:

901

AN:

248356

Hom.:

AF XY:

0.00373

AC XY:

504

AN XY:

135020

show subpopulations

Gnomad AFR exome

AF:

0.000259

Gnomad AMR exome

AF:

0.00150

Gnomad ASJ exome

AF:

0.00597

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000654

Gnomad FIN exome

AF:

0.0146

Gnomad NFE exome

AF:

0.00394

Gnomad OTH exome

AF:

0.00429

GnomAD4 exome

AF:

0.00353

AC:

5127

AN:

1451048

Hom.:

AF XY:

0.00347

AC XY:

2501

AN XY:

721700

show subpopulations

Gnomad4 AFR exome

AF:

0.000271

Gnomad4 AMR exome

AF:

0.00178

Gnomad4 ASJ exome

AF:

0.00518

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000813

Gnomad4 FIN exome

AF:

0.0155

Gnomad4 NFE exome

AF:

0.00354

Gnomad4 OTH exome

AF:

0.00281

GnomAD4 genome

AF:

0.00332

AC:

505

AN:

152038

Hom.:

Cov.:

AF XY:

0.00365

AC XY:

271

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.000530

Gnomad4 AMR

AF:

0.00296

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000416

Gnomad4 FIN

AF:

0.0146

Gnomad4 NFE

AF:

0.00375

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00407

Hom.:

Bravo

AF:

0.00239

Asia WGS

AF:

0.000289

AC:

AN:

3470

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Apr 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SPATA31C2: PM4:Supporting, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over