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 ENST00000706933.1(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
ENST00000706933.1 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

ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	Protein	UniProt
SPATA31C1	NM_001145124.1 link	c.3421C>T	p.Gln1141*	stop_gained	Exon 4 of 4	NP_001138596.1	P0DKV0-1
SPATA31C1	XM_011518702.1 link	c.3463C>T	p.Gln1155*	stop_gained	Exon 4 of 4	XP_011517004.1
LOC497256	NR_149022.1 link	n.472+9801G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31C1	ENST00000706933.1 link	c.3421C>T	p.Gln1141*	stop_gained	Exon 4 of 4			ENSP00000516655.1		P0DKV0-1

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 = 0.000000), 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 = 0.000000), 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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over