rs2668804

Positions:

• chr9-97735468-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000430058.2(PTCSC2):​n.331-12534G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,088 control chromosomes in the GnomAD database, including 11,220 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 0.37 (11220 hom., cov: 33)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

Genes affected

PTCSC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCSC2	NR_147055.1	n.778-10938G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCSC2	ENST00000430058.2	n.331-12534G>T		intron_variant		2
PTCSC2	ENST00000648027.1	n.471-10938G>T		intron_variant
PTCSC2	ENST00000648505.1	n.331-10938G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56804 AN: 151970 Hom.: 11209 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.374 AC: 56846 AN: 152088 Hom.: 11220 Cov.: 33 AF XY: 0.370 AC XY: 27482 AN XY: 74336

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.0464

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.348

Alfa AF: 0.397 Hom.: 2058

Bravo AF: 0.366

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	18
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2668804; hg19: chr9-100497750;