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.

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	UniProt
SAP30L	NM_024632.6	MANE Select	c.324+1094T>C	intron	N/A	NP_078908.1	Q9HAJ7-1
SAP30L	NM_001131062.2		c.202-1095T>C	intron	N/A	NP_001124534.1	Q9HAJ7-3
SAP30L	NM_001131063.2		c.202-1110T>C	intron	N/A	NP_001124535.1	Q9HAJ7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SAP30L	ENST00000297109.11	TSL:1 MANE Select	c.324+1094T>C	intron	N/A	ENSP00000297109.5	Q9HAJ7-1
SAP30L	ENST00000937072.1		c.324+1094T>C	intron	N/A	ENSP00000607131.1
SAP30L	ENST00000960937.1		c.324+1094T>C	intron	N/A	ENSP00000630996.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over