Genetic Variant NM_001353486.2:c.351+43C>T (chr9-4635232-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001353486.2(SPATA6L):c.351+43C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 1,469,260 control chromosomes in the GnomAD database, including 8,194 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 2189 hom., cov: 32)

Exomes 𝑓: 0.070 ( 6005 hom. )

Consequence

SPATA6L
NM_001353486.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.757

Publications

8 publications found

Variant links:

Genes affected

SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]

SPATA6L links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001353486.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SPATA6L	NM_001353486.2	MANE Select	c.351+43C>T	intron	N/A	NP_001340415.1
SPATA6L	NM_001353484.2		c.393+43C>T	intron	N/A	NP_001340413.1
SPATA6L	NM_001353485.2		c.393+43C>T	intron	N/A	NP_001340414.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SPATA6L	ENST00000682582.1	MANE Select	c.351+43C>T	intron	N/A	ENSP00000506787.1
SPATA6L	ENST00000451763.6	TSL:1	n.542+43C>T	intron	N/A
SPATA6L	ENST00000707146.1		c.393+43C>T	intron	N/A	ENSP00000516765.1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20618

AN:

151886

Hom.:

2176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.0548

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0686

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0550

Gnomad OTH

AF:

0.101

GnomAD2 exomes

AF:

0.102

AC:

14097

AN:

137746

AF XY:

0.0942

show subpopulations

Gnomad AFR exome

AF:

0.281

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.0529

Gnomad EAS exome

AF:

0.332

Gnomad FIN exome

AF:

0.0678

Gnomad NFE exome

AF:

0.0560

Gnomad OTH exome

AF:

0.0846

GnomAD4 exome

AF:

0.0702

AC:

92445

AN:

1317256

Hom.:

6005

Cov.:

AF XY:

0.0694

AC XY:

44845

AN XY:

646142

show subpopulations

African (AFR)

AF:

0.284

AC:

7399

AN:

26086

American (AMR)

AF:

0.151

AC:

2923

AN:

19416

Ashkenazi Jewish (ASJ)

AF:

0.0610

AC:

1216

AN:

19926

East Asian (EAS)

AF:

0.389

AC:

12336

AN:

31694

South Asian (SAS)

AF:

0.0931

AC:

5629

AN:

60450

European-Finnish (FIN)

AF:

0.0699

AC:

3492

AN:

49992

Middle Eastern (MID)

AF:

0.0879

AC:

461

AN:

5242

European-Non Finnish (NFE)

AF:

0.0515

AC:

54079

AN:

1050340

Other (OTH)

AF:

0.0907

AC:

4910

AN:

54110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

3453

6906

10358

13811

17264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2352

4704

7056

9408

11760

<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

AF:

0.136

AC:

20670

AN:

152004

Hom.:

2189

Cov.:

AF XY:

0.136

AC XY:

10136

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.274

AC:

11368

AN:

41422

American (AMR)

AF:

0.137

AC:

2098

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0548

AC:

190

AN:

3470

East Asian (EAS)

AF:

0.333

AC:

1711

AN:

5138

South Asian (SAS)

AF:

0.112

AC:

541

AN:

4812

European-Finnish (FIN)

AF:

0.0686

AC:

727

AN:

10594

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0551

AC:

3743

AN:

67970

Other (OTH)

AF:

0.106

AC:

223

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

811

1623

2434

3246

4057

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.0836

Hom.:

4027

Bravo

AF:

0.148

Asia WGS

AF:

0.249

AC:

864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.0

(source)

DANN

Benign

0.73

PhyloP100

0.76

Mutation Taster

=100/0

polymorphism (auto)

(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