Genetic Variant NM_015667.2:c.637C>T (chr9-61192723-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_015667.2(SPATA31A7):c.637C>T(p.Pro213Ser) 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 0.0032 ( 5 hom., cov: 6)

Exomes 𝑓: 0.0042 ( 510 hom. )

Failed GnomAD Quality Control

Consequence

SPATA31A7
NM_015667.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.06

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 -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0032767057).

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.637C>T	p.Pro213Ser	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.637C>T	p.Pro213Ser	missense	Exon 4 of 4	ENSP00000484807.1	Q8IWB4
SPATA31A7	ENST00000376458.6	TSL:5	n.454C>T		non_coding_transcript_exon	Exon 3 of 3
SPATA31A7	ENST00000614013.4	TSL:5	n.416C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.00322

AC:

124

AN:

38520

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000580

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00158

Gnomad ASJ

AF:

0.000822

Gnomad EAS

AF:

0.0969

Gnomad SAS

AF:

0.00302

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000162

Gnomad OTH

AF:

0.00200

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00416

AC:

3609

AN:

866964

Hom.:

510

Cov.:

AF XY:

0.00399

AC XY:

1750

AN XY:

439124

show subpopulations

African (AFR)

AF:

0.000710

AC:

AN:

22534

American (AMR)

AF:

0.00323

AC:

AN:

29728

Ashkenazi Jewish (ASJ)

AF:

0.000685

AC:

AN:

18972

East Asian (EAS)

AF:

0.0942

AC:

3082

AN:

32732

South Asian (SAS)

AF:

0.00150

AC:

AN:

59254

European-Finnish (FIN)

AF:

0.0000835

AC:

AN:

35922

Middle Eastern (MID)

AF:

0.000715

AC:

AN:

2796

European-Non Finnish (NFE)

AF:

0.0000976

AC:

AN:

625204

Other (OTH)

AF:

0.00620

AC:

247

AN:

39822

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

122

243

365

486

608

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<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:

0.00321

AC:

124

AN:

38576

Hom.:

Cov.:

AF XY:

0.00322

AC XY:

AN XY:

17726

show subpopulations

African (AFR)

AF:

0.000577

AC:

AN:

10394

American (AMR)

AF:

0.00158

AC:

AN:

3168

Ashkenazi Jewish (ASJ)

AF:

0.000822

AC:

AN:

1216

East Asian (EAS)

AF:

0.0972

AC:

106

AN:

1090

South Asian (SAS)

AF:

0.00300

AC:

AN:

666

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2620

Middle Eastern (MID)

AF:

0.00

AC:

AN:

104

European-Non Finnish (NFE)

AF:

0.000162

AC:

AN:

18540

Other (OTH)

AF:

0.00198

AC:

AN:

506

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.00118

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

0.086

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.030

(source)

DANN

Benign

0.26

DEOGEN2

Benign

0.027

LIST_S2

Benign

0.49

MetaRNN

Benign

0.0033

PhyloP100

-1.1

Sift4G

Benign

0.54

Vest4

0.090

gMVP

0.10

Mutation Taster

=100/0

polymorphism

(source)

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