dbSNP rs13029379: SCHLAP1:n.339-2597C>T (chr2-180721999-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000629145.1(SCHLAP1):n.339-2597C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 152,260 control chromosomes in the GnomAD database, including 703 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 0.086 ( 703 hom., cov: 32)

Consequence

SCHLAP1
ENST00000629145.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.635

Publications

8 publications found

Variant links:

Genes affected

SCHLAP1 (HGNC:48603): (SWI/SNF complex antagonist associated with prostate cancer 1)

SCHLAP1 links:

LOC105373771 (HGNC:):

LOC105373771 links:

Genome browser will be placed here

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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SCHLAP1	NR_104319.1 link	n.339-2597C>T	intron_variant	Intron 1 of 4
SCHLAP1	NR_104320.1 link	n.339-2597C>T	intron_variant	Intron 1 of 3
SCHLAP1	NR_104321.1 link	n.339-2597C>T	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SCHLAP1	ENST00000629145.1 link	n.339-2597C>T	intron_variant	Intron 1 of 4	1
SCHLAP1	ENST00000782824.1 link	n.431-2597C>T	intron_variant	Intron 1 of 4
SCHLAP1	ENST00000782825.1 link	n.434-2597C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0862

AC:

13108

AN:

152142

Hom.:

703

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0363

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0945

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.168

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0922

Gnomad OTH

AF:

0.0757

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0861

AC:

13117

AN:

152260

Hom.:

703

Cov.:

AF XY:

0.0888

AC XY:

6607

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0364

AC:

1515

AN:

41576

American (AMR)

AF:

0.103

AC:

1576

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0945

AC:

328

AN:

3470

East Asian (EAS)

AF:

0.129

AC:

667

AN:

5178

South Asian (SAS)

AF:

0.154

AC:

741

AN:

4826

European-Finnish (FIN)

AF:

0.168

AC:

1783

AN:

10582

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0922

AC:

6271

AN:

68026

Other (OTH)

AF:

0.0749

AC:

158

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

609

1218

1828

2437

3046

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0888

Hom.:

2383

Bravo

AF:

0.0799

Asia WGS

AF:

0.120

AC:

417

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.76

(source)

DANN

Benign

0.37

PhyloP100

-0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs13029379

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over