chr9-88129719-TCTG-T

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]

Genome browser will be placed here

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
SPATA31C2NM_001350978.3 linkc.3315_3317delCAG p.Ser1105del disruptive_inframe_deletion Exon 4 of 4 ENST00000324915.6 NP_001337907.1
SPATA31C2NM_001166137.1 linkc.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
SPATA31C2ENST00000324915.6 linkc.3315_3317delCAG p.Ser1105del disruptive_inframe_deletion Exon 4 of 4 6 NM_001350978.3 ENSP00000509734.1 A0A8I5KWQ5
SPATA31C2ENST00000675441.1 linkc.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.:
4
Cov.:
28
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.:
9
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.:
43
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.:
4
Cov.:
28
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.:
0
Bravo
AF:
0.00239
Asia WGS
AF:
0.000289
AC:
1
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.

Other links and lift over

dbSNP: rs545356666; hg19: chr9-90744634; API