chr9-97789486-G-A

Position:

• chr9-97789486-G-A

Variant summary

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

The NR_147055.1(PTCSC2):​n.777+14765C>T 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 0.343 in 151,946 control chromosomes in the GnomAD database, including 9,457 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 0.34 (9457 hom., cov: 32)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.777+14765C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.777+14765C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52070 AN: 151828 Hom.: 9442 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.343 AC: 52115 AN: 151946 Hom.: 9457 Cov.: 32 AF XY: 0.350 AC XY: 25970 AN XY: 74254

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.310

Alfa AF: 0.252 Hom.: 1019

Bravo AF: 0.341

Asia WGS AF: 0.473 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12352658; hg19: chr9-100551768;