rs7848973

chr9-97826557-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.166-16518T>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 0.669 in 152,084 control chromosomes in the GnomAD database, including 34,800 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 0.67 (34800 hom., cov: 32)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.166-16518T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.166-16518T>C		intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000649526.1	n.166-16518T>C		intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000650104.1	n.165+26359T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101679 AN: 151966 Hom.: 34767 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.669 AC: 101758 AN: 152084 Hom.: 34800 Cov.: 32 AF XY: 0.672 AC XY: 49978 AN XY: 74340

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.666

Alfa AF: 0.615 Hom.: 57884

Bravo AF: 0.679

Asia WGS AF: 0.806 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7848973; hg19: chr9-100588839;