9-42183738-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001145196.1(SPATA31A6):​c.51C>T​(p.Asn17Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000411 in 1,534,826 control chromosomes in the GnomAD database, including 104 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00027 ( 3 hom., cov: 23)
Exomes 𝑓: 0.00042 ( 101 hom. )

Consequence

SPATA31A6
NM_001145196.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.278
Variant links:
Genes affected
SPATA31A6 (HGNC:32006): (SPATA31 subfamily A member 6) Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 9-42183738-C-T is Benign according to our data. Variant chr9-42183738-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659218.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.278 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPATA31A6NM_001145196.1 linkc.51C>T p.Asn17Asn synonymous_variant Exon 1 of 4 ENST00000332857.7 NP_001138668.1 Q5VVP1
SPATA31A6XM_011517871.4 linkc.51C>T p.Asn17Asn synonymous_variant Exon 1 of 4 XP_011516173.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPATA31A6ENST00000332857.7 linkc.51C>T p.Asn17Asn synonymous_variant Exon 1 of 4 1 NM_001145196.1 ENSP00000329825.6 Q5VVP1

Frequencies

GnomAD3 genomes
AF:
0.000269
AC:
36
AN:
133648
Hom.:
3
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.000154
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000448
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000247
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000315
Gnomad OTH
AF:
0.00219
GnomAD4 exome
AF:
0.000425
AC:
595
AN:
1401178
Hom.:
101
Cov.:
34
AF XY:
0.000409
AC XY:
285
AN XY:
697382
show subpopulations
Gnomad4 AFR exome
AF:
0.000136
Gnomad4 AMR exome
AF:
0.000420
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000537
Gnomad4 SAS exome
AF:
0.000444
Gnomad4 FIN exome
AF:
0.0000829
Gnomad4 NFE exome
AF:
0.000466
Gnomad4 OTH exome
AF:
0.000521
GnomAD4 genome
AF:
0.000269
AC:
36
AN:
133648
Hom.:
3
Cov.:
23
AF XY:
0.000216
AC XY:
14
AN XY:
64868
show subpopulations
Gnomad4 AFR
AF:
0.000154
Gnomad4 AMR
AF:
0.000448
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000247
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000315
Gnomad4 OTH
AF:
0.00219
Alfa
AF:
0.000409
Hom.:
3

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jul 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

SPATA31A6: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
7.2
DANN
Benign
0.90

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: rs746632976; hg19: chr9-40700370; API