rs11688866

Variant names:

• chr2-180741180-A-G
• rs11688866
• ENST00000629145.1:n.433+16490A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000629145.1(SCHLAP1):​n.433+16490A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,886 control chromosomes in the GnomAD database, including 17,546 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 0.48 (17546 hom., cov: 31)
• Consequence: SCHLAP1 ENST00000629145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCHLAP1	NR_104319.1	n.433+16490A>G		intron_variant	Intron 2 of 4
SCHLAP1	NR_104320.1	n.433+16490A>G		intron_variant	Intron 2 of 3
SCHLAP1	NR_104321.1	n.433+16490A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCHLAP1	ENST00000629145.1	n.433+16490A>G		intron_variant	Intron 2 of 4	1
SCHLAP1	ENST00000782824.1	n.626+15889A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72301 AN: 151770 Hom.: 17532 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.476 AC: 72357 AN: 151886 Hom.: 17546 Cov.: 31 AF XY: 0.480 AC XY: 35662 AN XY: 74242

African (AFR) AF: 0.386 AC: 15968 AN: 41386

American (AMR) AF: 0.544 AC: 8303 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1851 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2310 AN: 5158

South Asian (SAS) AF: 0.478 AC: 2300 AN: 4808

European-Finnish (FIN) AF: 0.543 AC: 5729 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34409 AN: 67922

Other (OTH) AF: 0.443 AC: 933 AN: 2106

Alfa AF: 0.489 Hom.: 6956

Bravo AF: 0.472

Asia WGS AF: 0.428 AC: 1489 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.28
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11688866; hg19: chr2-181605907;