Genetic Variant NM_001145196.1:c.51C>A (chr9-42183738-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001145196.1(SPATA31A6):c.51C>A(p.Asn17Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 133,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. N17N) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0000075 ( 0 hom., cov: 23)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SPATA31A6
NM_001145196.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.278

Publications

0 publications found

Variant links:

Genes affected

SPATA31A6 (HGNC:32006): (SPATA31 subfamily A member 6) Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

SPATA31A6 links:

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ACMG classification

Classification was made for transcript

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

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.24945384).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145196.1. 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
	SPATA31A6	NM_001145196.1	MANE Select	c.51C>A	p.Asn17Lys	missense	Exon 1 of 4	NP_001138668.1	Q5VVP1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31A6	ENST00000332857.7	TSL:1 MANE Select	c.51C>A	p.Asn17Lys	missense	Exon 1 of 4	ENSP00000329825.6	Q5VVP1

Frequencies

GnomAD3 genomes

AF:

0.00000748

AC:

AN:

133650

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000309

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: AC0

AF:

0.00

AC:

AN:

1401178

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

697382

African (AFR)

AF:

0.00

AC:

AN:

29314

American (AMR)

AF:

0.00

AC:

AN:

42818

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24668

East Asian (EAS)

AF:

0.00

AC:

AN:

37268

South Asian (SAS)

AF:

0.00

AC:

AN:

83288

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48272

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3980

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1073948

Other (OTH)

AF:

0.00

AC:

AN:

57622

GnomAD4 genome

AF:

0.00000748

AC:

AN:

133650

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

64868

show subpopulations

African (AFR)

AF:

0.0000309

AC:

AN:

32404

American (AMR)

AF:

0.00

AC:

AN:

13408

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3192

East Asian (EAS)

AF:

0.00

AC:

AN:

4428

South Asian (SAS)

AF:

0.00

AC:

AN:

4052

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

296

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

63564

Other (OTH)

AF:

0.00

AC:

AN:

1830

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.825

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.:

Bravo

AF:

0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.0092

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.99

FATHMM_MKL

Benign

0.0062

LIST_S2

Benign

0.51

M_CAP

Benign

0.0018

MetaRNN

Benign

0.25

MetaSVM

Benign

-1.1

PhyloP100

0.28

PrimateAI

Benign

0.36

PROVEAN

Benign

-0.92

Sift

Pathogenic

0.0

Sift4G

Uncertain

0.036

Vest4

0.60

MutPred

0.30

Gain of ubiquitination at N17 (P = 0.0109)

MVP

0.030

ClinPred

0.30

GERP RS

0.11

PromoterAI

0.0084

Neutral

(source)

gMVP

0.10

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

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over