9-97776188-A-G

Position:

• chr9-97776188-A-G

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.330+29652T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 151,920 control chromosomes in the GnomAD database, including 40,196 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 (40196 hom., cov: 30)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696

Genes affected

PTCSC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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+28063T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCSC2	ENST00000430058.2	n.330+29652T>C		intron_variant		2
PTCSC2	ENST00000648027.1	n.470+28063T>C		intron_variant
PTCSC2	ENST00000648505.1	n.330+29652T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109662 AN: 151802 Hom.: 40159 Cov.: 30

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.722 AC: 109755 AN: 151920 Hom.: 40196 Cov.: 30 AF XY: 0.726 AC XY: 53881 AN XY: 74250

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.720

Alfa AF: 0.693 Hom.: 6285

Bravo AF: 0.730

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7028661; hg19: chr9-100538470;