rs1877431

chr9-97771865-A-G

Variant summary

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

The NR_147055.1(PTCSC2):n.777+32386T>C 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 0.663 in 151,764 control chromosomes in the GnomAD database, including 33,878 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 0.66 (33878 hom., cov: 30)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536

Genes affected

PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.777+32386T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.777+32386T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100526 AN: 151646 Hom.: 33845 Cov.: 30

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.663 AC: 100609 AN: 151764 Hom.: 33878 Cov.: 30 AF XY: 0.667 AC XY: 49454 AN XY: 74146

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.668

Alfa AF: 0.643 Hom.: 11736

Bravo AF: 0.671

Asia WGS AF: 0.791 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	14
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1877431; hg19: chr9-100534147;