rs2808699

Positions:

• chr9-97743548-C-A

Variant summary

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

The ENST00000562653.1(ENSG00000260677):​n.341C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,946 control chromosomes in the GnomAD database, including 10,634 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 0.36 (10634 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000562653.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

Genes affected

(HGNC:):

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=-0.89).
• 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	UniProt
PTCSC2	NR_147055.1	n.778-19018G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000562653.1	n.341C>A		non_coding_transcript_exon_variant	1/1
PTCSC2	ENST00000649461.1	n.778-19018G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55041 AN: 151828 Hom.: 10622 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.340

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.363 AC: 55081 AN: 151946 Hom.: 10634 Cov.: 32 AF XY: 0.359 AC XY: 26633 AN XY: 74240

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.0474

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.340

Alfa AF: 0.407 Hom.: 16782

Bravo AF: 0.352

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2808699; hg19: chr9-100505830;