Genetic Variant NM_024632.6:c.324+117G>A (chr5-154451330-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_024632.6(SAP30L):c.324+117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 1,127,616 control chromosomes in the GnomAD database, including 240,623 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 0.63 ( 30936 hom., cov: 32)

Exomes 𝑓: 0.65 ( 209687 hom. )

Consequence

SAP30L
NM_024632.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.829

Publications

5 publications found

Variant links:

Genes affected

SAP30L (HGNC:25663): (SAP30 like) Enables several functions, including non-sequence-specific DNA binding activity, bending; phosphatidylinositol phosphate binding activity; and zinc ion binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Apr 2022]

SAP30L 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=-0.77).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024632.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SAP30L	NM_024632.6	MANE Select	c.324+117G>A	intron	N/A	NP_078908.1
SAP30L	NM_001131062.2		c.202-2072G>A	intron	N/A	NP_001124534.1
SAP30L	NM_001131063.2		c.202-2087G>A	intron	N/A	NP_001124535.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SAP30L	ENST00000297109.11	TSL:1 MANE Select	c.324+117G>A	intron	N/A	ENSP00000297109.5
SAP30L	ENST00000937072.1		c.324+117G>A	intron	N/A	ENSP00000607131.1
SAP30L	ENST00000960937.1		c.324+117G>A	intron	N/A	ENSP00000630996.1

Frequencies

GnomAD3 genomes

AF:

0.635

AC:

96413

AN:

151940

Hom.:

30922

Cov.:

show subpopulations

Gnomad AFR

AF:

0.550

Gnomad AMI

AF:

0.767

Gnomad AMR

AF:

0.732

Gnomad ASJ

AF:

0.658

Gnomad EAS

AF:

0.600

Gnomad SAS

AF:

0.656

Gnomad FIN

AF:

0.669

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.656

Gnomad OTH

AF:

0.667

GnomAD4 exome

AF:

0.654

AC:

637586

AN:

975558

Hom.:

209687

Cov.:

AF XY:

0.654

AC XY:

319287

AN XY:

488524

show subpopulations

African (AFR)

AF:

0.539

AC:

12182

AN:

22584

American (AMR)

AF:

0.789

AC:

16944

AN:

21476

Ashkenazi Jewish (ASJ)

AF:

0.655

AC:

11136

AN:

17002

East Asian (EAS)

AF:

0.581

AC:

20686

AN:

35612

South Asian (SAS)

AF:

0.658

AC:

37291

AN:

56664

European-Finnish (FIN)

AF:

0.660

AC:

30877

AN:

46768

Middle Eastern (MID)

AF:

0.638

AC:

2446

AN:

3832

European-Non Finnish (NFE)

AF:

0.656

AC:

478044

AN:

728546

Other (OTH)

AF:

0.650

AC:

27980

AN:

43074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

10836

21672

32507

43343

54179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11186

22372

33558

44744

55930

<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:

0.634

AC:

96455

AN:

152058

Hom.:

30936

Cov.:

AF XY:

0.636

AC XY:

47297

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.549

AC:

22741

AN:

41446

American (AMR)

AF:

0.733

AC:

11196

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.658

AC:

2285

AN:

3472

East Asian (EAS)

AF:

0.600

AC:

3101

AN:

5170

South Asian (SAS)

AF:

0.657

AC:

3163

AN:

4812

European-Finnish (FIN)

AF:

0.669

AC:

7065

AN:

10562

Middle Eastern (MID)

AF:

0.619

AC:

182

AN:

294

European-Non Finnish (NFE)

AF:

0.656

AC:

44609

AN:

67992

Other (OTH)

AF:

0.669

AC:

1415

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1795

3590

5385

7180

8975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<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:

0.652

Hom.:

109427

Bravo

AF:

0.641

Asia WGS

AF:

0.624

AC:

2167

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

9.9

(source)

DANN

Benign

0.69

PhyloP100

0.83

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