Genetic Variant SPATA31A7:p.Ala279Val (chr9-61192922-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_015667.2(SPATA31A7):c.836C>T(p.Ala279Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000042 ( 0 hom., cov: 5)

Exomes 𝑓: 0.000037 ( 4 hom. )

Failed GnomAD Quality Control

Consequence

SPATA31A7
NM_015667.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.159

Publications

0 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 -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.069309205).

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.836C>T	p.Ala279Val	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.836C>T	p.Ala279Val	missense	Exon 4 of 4	ENSP00000484807.1	Q8IWB4
SPATA31A7	ENST00000618860.4	TSL:5	n.687C>T		non_coding_transcript_exon	Exon 3 of 3
SPATA31A7	ENST00000621711.1	TSL:5	n.234+466C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000424

AC:

AN:

23580

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000462

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000176

AC:

AN:

113380

AF XY:

0.0000165

show subpopulations

Gnomad AFR exome

AF:

0.000153

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000193

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000366

AC:

AN:

901070

Hom.:

Cov.:

AF XY:

0.0000243

AC XY:

AN XY:

452328

show subpopulations

African (AFR)

AF:

0.000367

AC:

AN:

19090

American (AMR)

AF:

0.000830

AC:

AN:

27704

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18972

East Asian (EAS)

AF:

0.00

AC:

AN:

31752

South Asian (SAS)

AF:

0.00

AC:

AN:

55514

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30736

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2776

European-Non Finnish (NFE)

AF:

0.00000445

AC:

AN:

674100

Other (OTH)

AF:

0.00

AC:

AN:

40426

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000424

AC:

AN:

23580

Hom.:

Cov.:

AF XY:

0.0000924

AC XY:

AN XY:

10818

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

4266

American (AMR)

AF:

0.000462

AC:

AN:

2164

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

850

East Asian (EAS)

AF:

0.00

AC:

AN:

690

South Asian (SAS)

AF:

0.00

AC:

AN:

386

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1806

Middle Eastern (MID)

AF:

0.00

AC:

AN:

100

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

12752

Other (OTH)

AF:

0.00

AC:

AN:

326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

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:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

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

0.095

BayesDel_noAF

Benign

-0.53

CADD

Benign

1.8

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.029

LIST_S2

Benign

0.50

MetaRNN

Benign

0.069

PhyloP100

0.16

Sift4G

Benign

0.22

Vest4

0.073

gMVP

0.066

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

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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