Genetic Variant SPATA31A7:p.Pro211Ser (chr9-61192717-C-T) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_015667.2(SPATA31A7):c.631C>T(p.Pro211Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0075 ( 0 hom., cov: 6)

Exomes 𝑓: 0.0086 ( 144 hom. )

Failed GnomAD Quality Control

Consequence

SPATA31A7
NM_015667.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.469

Publications

1 publications found

Variant links:

Genes affected

SPATA31A7 (HGNC:32007): (SPATA31 subfamily A member 7) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA31A7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008683622).

BP6

Variant 9-61192717-C-T is Benign according to our data. Variant chr9-61192717-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2205976.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015667.2. 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
	SPATA31A7	NM_015667.2	MANE Select	c.631C>T	p.Pro211Ser	missense	Exon 4 of 4	NP_056482.2	Q8IWB4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SPATA31A7	ENST00000619167.2	TSL:1 MANE Select	c.631C>T	p.Pro211Ser	missense	Exon 4 of 4	ENSP00000484807.1	Q8IWB4
SPATA31A7	ENST00000376458.6	TSL:5	n.448C>T		non_coding_transcript_exon	Exon 3 of 3
SPATA31A7	ENST00000614013.4	TSL:5	n.410C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.00749

AC:

296

AN:

39514

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00141

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00476

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00294

Gnomad FIN

AF:

0.0117

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0121

Gnomad OTH

AF:

0.00196

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00864

AC:

7920

AN:

916536

Hom.:

144

Cov.:

AF XY:

0.00856

AC XY:

3969

AN XY:

463594

show subpopulations

African (AFR)

AF:

0.00165

AC:

AN:

23632

American (AMR)

AF:

0.00301

AC:

AN:

31200

Ashkenazi Jewish (ASJ)

AF:

0.00158

AC:

AN:

19640

East Asian (EAS)

AF:

0.00

AC:

AN:

33568

South Asian (SAS)

AF:

0.00136

AC:

AN:

61864

European-Finnish (FIN)

AF:

0.0121

AC:

457

AN:

37864

Middle Eastern (MID)

AF:

0.00242

AC:

AN:

2898

European-Non Finnish (NFE)

AF:

0.0104

AC:

6937

AN:

664274

Other (OTH)

AF:

0.00652

AC:

271

AN:

41596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

281

562

844

1125

1406

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

196

392

588

784

980

<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:

0.00746

AC:

295

AN:

39568

Hom.:

Cov.:

AF XY:

0.00702

AC XY:

128

AN XY:

18244

show subpopulations

African (AFR)

AF:

0.00140

AC:

AN:

10688

American (AMR)

AF:

0.00475

AC:

AN:

3160

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1226

East Asian (EAS)

AF:

0.00

AC:

AN:

1146

South Asian (SAS)

AF:

0.00147

AC:

AN:

682

European-Finnish (FIN)

AF:

0.0117

AC:

AN:

2658

Middle Eastern (MID)

AF:

0.00

AC:

AN:

102

European-Non Finnish (NFE)

AF:

0.0121

AC:

232

AN:

19110

Other (OTH)

AF:

0.00195

AC:

AN:

514

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00649

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.61

(source)

DANN

Benign

0.40

DEOGEN2

Benign

0.031

LIST_S2

Benign

0.48

MetaRNN

Benign

0.0087

PhyloP100

-0.47

Sift4G

Benign

0.12

Vest4

0.054

gMVP

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over