Genetic Variant SAP30L:c.324+1094T>C (chr5-154452307-T-C) – 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+1094T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 208,702 control chromosomes in the GnomAD database, including 4,674 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 0.19 ( 3261 hom., cov: 29)

Exomes 𝑓: 0.22 ( 1413 hom. )

Consequence

SAP30L
NM_024632.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143

Publications

13 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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAP30L	NM_024632.6 link	c.324+1094T>C		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+1094T>C		intron_variant	Intron 2 of 3	1	NM_024632.6	ENSP00000297109.5		Q9HAJ7-1

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28081

AN:

148518

Hom.:

3245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0826

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.211

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.199

GnomAD4 exome

AF:

0.218

AC:

13125

AN:

60076

Hom.:

1413

AF XY:

0.218

AC XY:

6369

AN XY:

29172

show subpopulations

African (AFR)

AF:

0.0846

AC:

AN:

1052

American (AMR)

AF:

0.433

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.290

AC:

102

AN:

352

East Asian (EAS)

AF:

0.230

AC:

AN:

230

South Asian (SAS)

AF:

0.266

AC:

304

AN:

1142

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.246

AC:

AN:

130

European-Non Finnish (NFE)

AF:

0.220

AC:

12149

AN:

55244

Other (OTH)

AF:

0.198

AC:

365

AN:

1846

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

539

1077

1616

2154

2693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.189

AC:

28124

AN:

148626

Hom.:

3261

Cov.:

AF XY:

0.194

AC XY:

14032

AN XY:

72232

show subpopulations

African (AFR)

AF:

0.0824

AC:

3283

AN:

39842

American (AMR)

AF:

0.360

AC:

5390

AN:

14952

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

802

AN:

3462

East Asian (EAS)

AF:

0.263

AC:

1338

AN:

5078

South Asian (SAS)

AF:

0.225

AC:

1063

AN:

4716

European-Finnish (FIN)

AF:

0.192

AC:

1864

AN:

9690

Middle Eastern (MID)

AF:

0.216

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.201

AC:

13590

AN:

67642

Other (OTH)

AF:

0.205

AC:

423

AN:

2060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1025

2050

3076

4101

5126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.208

Hom.:

4163

Bravo

AF:

0.201

Asia WGS

AF:

0.262

AC:

909

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.8

(source)

DANN

Benign

0.41

PhyloP100

0.14

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