Genetic Variant SPATS2L:c.39+165A>G (chr2-200389448-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001100423.2(SPATS2L):c.39+165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 533,408 control chromosomes in the GnomAD database, including 126,559 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 0.65 ( 32773 hom., cov: 33)

Exomes 𝑓: 0.70 ( 93786 hom. )

Consequence

SPATS2L
NM_001100423.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.480

Publications

5 publications found

Variant links:

Genes affected

SPATS2L (HGNC:24574): (spermatogenesis associated serine rich 2 like) Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

SPATS2L links:

Genome browser will be placed here

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001100423.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SPATS2L	NM_001100423.2	MANE Select	c.39+165A>G	intron	N/A	NP_001093893.1	Q9NUQ6-1
SPATS2L	NM_001282744.2		c.129+165A>G	intron	N/A	NP_001269673.1	Q9NUQ6-3
SPATS2L	NM_001100422.1		c.39+165A>G	intron	N/A	NP_001093892.1	Q9NUQ6-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SPATS2L	ENST00000409140.8	TSL:2 MANE Select	c.39+165A>G	intron	N/A	ENSP00000386730.3	Q9NUQ6-1
SPATS2L	ENST00000358677.9	TSL:1	c.39+165A>G	intron	N/A	ENSP00000351503.4	Q9NUQ6-1
SPATS2L	ENST00000360760.9	TSL:1	c.39+165A>G	intron	N/A	ENSP00000353989.5	Q9NUQ6-2

Frequencies

GnomAD3 genomes

AF:

0.645

AC:

98121

AN:

152036

Hom.:

32747

Cov.:

show subpopulations

Gnomad AFR

AF:

0.463

Gnomad AMI

AF:

0.653

Gnomad AMR

AF:

0.741

Gnomad ASJ

AF:

0.733

Gnomad EAS

AF:

0.675

Gnomad SAS

AF:

0.811

Gnomad FIN

AF:

0.722

Gnomad MID

AF:

0.682

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.650

GnomAD4 exome

AF:

0.698

AC:

266265

AN:

381254

Hom.:

93786

Cov.:

AF XY:

0.703

AC XY:

140637

AN XY:

200036

show subpopulations

African (AFR)

AF:

0.477

AC:

5203

AN:

10902

American (AMR)

AF:

0.761

AC:

9897

AN:

13012

Ashkenazi Jewish (ASJ)

AF:

0.736

AC:

8863

AN:

12038

East Asian (EAS)

AF:

0.660

AC:

18568

AN:

28122

South Asian (SAS)

AF:

0.794

AC:

23290

AN:

29342

European-Finnish (FIN)

AF:

0.696

AC:

21272

AN:

30564

Middle Eastern (MID)

AF:

0.702

AC:

2342

AN:

3338

European-Non Finnish (NFE)

AF:

0.697

AC:

161406

AN:

231412

Other (OTH)

AF:

0.685

AC:

15424

AN:

22524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

3596

7191

10787

14382

17978

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

740

1480

2220

2960

3700

<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:

0.645

AC:

98200

AN:

152154

Hom.:

32773

Cov.:

AF XY:

0.656

AC XY:

48774

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.464

AC:

19256

AN:

41496

American (AMR)

AF:

0.741

AC:

11330

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.733

AC:

2544

AN:

3472

East Asian (EAS)

AF:

0.675

AC:

3493

AN:

5176

South Asian (SAS)

AF:

0.811

AC:

3914

AN:

4828

European-Finnish (FIN)

AF:

0.722

AC:

7645

AN:

10586

Middle Eastern (MID)

AF:

0.675

AC:

197

AN:

292

European-Non Finnish (NFE)

AF:

0.704

AC:

47852

AN:

67988

Other (OTH)

AF:

0.650

AC:

1375

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1705

3410

5114

6819

8524

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.684

Hom.:

51740

Bravo

AF:

0.636

Asia WGS

AF:

0.720

AC:

2505

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.14

(source)

DANN

Benign

0.38

PhyloP100

-0.48

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