Genetic Variant SPATA31A7:p.Ala287Ser (chr9-61192945-G-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.859G>T(p.Ala287Ser) 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 Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 5)

Exomes 𝑓: 0.000060 ( 9 hom. )

Failed GnomAD Quality Control

Consequence

SPATA31A7
NM_015667.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.344

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=0.09076306).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31A7	NM_015667.2 link	c.859G>T	p.Ala287Ser	missense_variant	Exon 4 of 4	ENST00000619167.2	NP_056482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31A7	ENST00000619167.2 link	c.859G>T	p.Ala287Ser	missense_variant	Exon 4 of 4	1	NM_015667.2	ENSP00000484807.1		Q8IWB4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

23290

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

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

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000598

AC:

AN:

1036472

Hom.:

Cov.:

AF XY:

0.0000540

AC XY:

AN XY:

518548

show subpopulations

African (AFR)

AF:

0.0000457

AC:

AN:

21894

American (AMR)

AF:

0.000316

AC:

AN:

31630

Ashkenazi Jewish (ASJ)

AF:

0.00147

AC:

AN:

21020

East Asian (EAS)

AF:

0.00

AC:

AN:

33166

South Asian (SAS)

AF:

0.00

AC:

AN:

61954

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32596

Middle Eastern (MID)

AF:

0.000658

AC:

AN:

3040

European-Non Finnish (NFE)

AF:

0.0000140

AC:

AN:

786404

Other (OTH)

AF:

0.000156

AC:

AN:

44768

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

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: AC0;AS_VQSR

AF:

0.00

AC:

AN:

23290

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

10742

African (AFR)

AF:

0.00

AC:

AN:

4094

American (AMR)

AF:

0.00

AC:

AN:

2046

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

836

East Asian (EAS)

AF:

0.00

AC:

AN:

606

South Asian (SAS)

AF:

0.00

AC:

AN:

354

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1698

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

13018

Other (OTH)

AF:

0.00

AC:

AN:

314

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

May 17, 2023

Ambry Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.859G>T (p.A287S) alteration is located in exon 4 (coding exon 4) of the SPATA31A7 gene. This alteration results from a G to T substitution at nucleotide position 859, causing the alanine (A) at amino acid position 287 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_noAF

Benign

-1.0

CADD

Benign

4.7

(source)

DANN

Benign

0.94

DEOGEN2

Benign

0.063

LIST_S2

Benign

0.42

MetaRNN

Benign

0.091

PhyloP100

-0.34

Sift4G

Benign

0.066

Vest4

0.19

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over