rs13029379

Positions:

• chr2-180721999-C-T

Variant summary

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

The NR_104322.1(SCHLAP1):​n.339-2597C>T 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 0.0861 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 NR_104322.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

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

LOC105373771 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
SCHLAP1	NR_104322.1	n.339-2597C>T		intron_variant, non_coding_transcript_variant
LOC105373771	XR_923638.3	n.257+905G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCHLAP1	ENST00000629145.1	n.339-2597C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13108 AN: 152142 Hom.: 703 Cov.: 32

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.: 32 AF XY: 0.0888 AC XY: 6607 AN XY: 74418

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.0922

Gnomad4 OTH AF: 0.0749

Alfa AF: 0.0902 Hom.: 1582

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
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13029379; hg19: chr2-181586726;