9-97784318-C-T

Position:

• chr9-97784318-C-T

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.330+21522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,018 control chromosomes in the GnomAD database, including 39,548 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 0.72 (39548 hom., cov: 31)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

PTCSC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCSC2	NR_147055.1	n.777+19933G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCSC2	ENST00000430058.2	n.330+21522G>A		intron_variant		2
PTCSC2	ENST00000648027.1	n.470+19933G>A		intron_variant
PTCSC2	ENST00000648505.1	n.330+21522G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108924 AN: 151900 Hom.: 39520 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.717 AC: 109007 AN: 152018 Hom.: 39548 Cov.: 31 AF XY: 0.721 AC XY: 53541 AN XY: 74274

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.718

Alfa AF: 0.679 Hom.: 49578

Bravo AF: 0.724

Asia WGS AF: 0.802 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925489; hg19: chr9-100546600;