Variant rs2277939 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SAP30L	NM_024632.6 link	c.324+117G>A		intron_variant		ENST00000297109.11	NP_078908.1	Q9HAJ7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAP30L	ENST00000297109.11 link	c.324+117G>A		intron_variant		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

Gnomad4 AFR exome

AF:

0.539

Gnomad4 AMR exome

AF:

0.789

Gnomad4 ASJ exome

AF:

0.655

Gnomad4 EAS exome

AF:

0.581

Gnomad4 SAS exome

AF:

0.658

Gnomad4 FIN exome

AF:

0.660

Gnomad4 NFE exome

AF:

0.656

Gnomad4 OTH exome

AF:

0.650

GnomAD4 genome

AF:

0.634

AC:

96455

AN:

152058

Hom.:

30936

Cov.:

AF XY:

0.636

AC XY:

47297

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.549

Gnomad4 AMR

AF:

0.733

Gnomad4 ASJ

AF:

0.658

Gnomad4 EAS

AF:

0.600

Gnomad4 SAS

AF:

0.657

Gnomad4 FIN

AF:

0.669

Gnomad4 NFE

AF:

0.656

Gnomad4 OTH

AF:

0.669

Alfa

AF:

0.656

Hom.:

67004

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

DANN

Benign

0.69

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over