9-97820913-C-T

Variant summary

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

The NR_147055.1(PTCSC2):n.166-10874G>A 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 0.658 in 151,970 control chromosomes in the GnomAD database, including 33,698 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 (33698 hom., cov: 31)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.166-10874G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.166-10874G>A		intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000649526.1	n.166-10874G>A		intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000650104.1	n.165+32003G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99856 AN: 151852 Hom.: 33665 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.658 AC: 99935 AN: 151970 Hom.: 33698 Cov.: 31 AF XY: 0.660 AC XY: 49021 AN XY: 74270

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.661

Alfa AF: 0.633 Hom.: 6032

Bravo AF: 0.671

Asia WGS AF: 0.805 AC: 2803 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	0.35
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443432; hg19: chr9-100583195;