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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAP30L	NM_024632.6 link	c.324+117G>A		intron_variant	Intron 2 of 3	ENST00000297109.11	NP_078908.1	Q9HAJ7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAP30L	ENST00000297109.11 link	c.324+117G>A		intron_variant	Intron 2 of 3	1	NM_024632.6	ENSP00000297109.5		Q9HAJ7-1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over