rs11688866

Positions:

• chr2-180741180-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104322.1(SCHLAP1):​n.534+15889A>G variant causes a intron, non coding transcript 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 NR_104322.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SCHLAP1	NR_104322.1	n.534+15889A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCHLAP1	ENST00000629145.1	n.433+16490A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.443

Alfa AF: 0.483 Hom.: 4304

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11688866; hg19: chr2-181605907;