dbSNP rs595203: SPATA31C1:p.Gln1141* (chr9-87923328-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001145124.1(SPATA31C1):c.3421C>T(p.Gln1141*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0098 ( 11 hom., cov: 28)

Exomes 𝑓: 0.0034 ( 126 hom. )

Failed GnomAD Quality Control

Consequence

SPATA31C1
NM_001145124.1 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.403

Publications

1 publications found

Variant links:

COSMIC-nc: COSV69665900

Genes affected

SPATA31C1 (HGNC:27846): (SPATA31 subfamily C member 1) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA31C1 links:

ENSG00000289459 (HGNC:):

ENSG00000289459 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001145124.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145124.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31C1	NM_001145124.1	MANE Select	c.3421C>T	p.Gln1141*	stop_gained	Exon 4 of 4	NP_001138596.1	P0DKV0-1
	LOC497256	NR_149022.1		n.472+9801G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SPATA31C1	ENST00000706933.1	MANE Select	c.3421C>T	p.Gln1141*	stop_gained	Exon 4 of 4	ENSP00000516655.1	P0DKV0-1
ENSG00000289459	ENST00000783875.1		n.174+9801G>A		intron	N/A
ENSG00000289459	ENST00000783876.1		n.347+9801G>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00978

AC:

1456

AN:

148858

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00369

Gnomad AMI

AF:

0.0150

Gnomad AMR

AF:

0.00927

Gnomad ASJ

AF:

0.0111

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000629

Gnomad FIN

AF:

0.00713

Gnomad MID

AF:

0.0163

Gnomad NFE

AF:

0.0153

Gnomad OTH

AF:

0.00876

GnomAD2 exomes

AF:

0.00165

AC:

408

AN:

247644

AF XY:

0.00157

show subpopulations

Gnomad AFR exome

AF:

0.000845

Gnomad AMR exome

AF:

0.00218

Gnomad ASJ exome

AF:

0.00210

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000232

Gnomad NFE exome

AF:

0.00235

Gnomad OTH exome

AF:

0.00449

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00337

AC:

4853

AN:

1442034

Hom.:

126

Cov.:

AF XY:

0.00322

AC XY:

2312

AN XY:

717038

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00115

AC:

AN:

33136

American (AMR)

AF:

0.00386

AC:

170

AN:

44086

Ashkenazi Jewish (ASJ)

AF:

0.00722

AC:

183

AN:

25334

East Asian (EAS)

AF:

0.000102

AC:

AN:

39180

South Asian (SAS)

AF:

0.000825

AC:

AN:

86028

European-Finnish (FIN)

AF:

0.00421

AC:

217

AN:

51524

Middle Eastern (MID)

AF:

0.00283

AC:

AN:

5644

European-Non Finnish (NFE)

AF:

0.00351

AC:

3857

AN:

1098150

Other (OTH)

AF:

0.00504

AC:

297

AN:

58952

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.255

Heterozygous variant carriers

517

1035

1552

2070

2587

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00977

AC:

1456

AN:

148976

Hom.:

Cov.:

AF XY:

0.00936

AC XY:

682

AN XY:

72840

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00371

AC:

152

AN:

41022

American (AMR)

AF:

0.00926

AC:

138

AN:

14908

Ashkenazi Jewish (ASJ)

AF:

0.0111

AC:

AN:

3412

East Asian (EAS)

AF:

0.00

AC:

AN:

5080

South Asian (SAS)

AF:

0.000420

AC:

AN:

4764

European-Finnish (FIN)

AF:

0.00713

AC:

AN:

10376

Middle Eastern (MID)

AF:

0.0176

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.0154

AC:

1016

AN:

66186

Other (OTH)

AF:

0.00867

AC:

AN:

2076

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.283

Heterozygous variant carriers

121

243

364

486

607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0151

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Pathogenic

(source)

DANN

Benign

0.80

PhyloP100

-0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over