rs7030241

Positions:

• chr9-97788093-T-A
• chr9-97788093-T-C
• chr9-97788093-T-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+16158A>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 0.719 in 152,004 control chromosomes in the GnomAD database, including 39,826 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 0.72 (39826 hom., cov: 30)
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.777+16158A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.777+16158A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109277 AN: 151886 Hom.: 39799 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.719 AC: 109357 AN: 152004 Hom.: 39826 Cov.: 30 AF XY: 0.723 AC XY: 53723 AN XY: 74288

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.718

Alfa AF: 0.591 Hom.: 1777

Bravo AF: 0.727

Asia WGS AF: 0.803 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7030241; hg19: chr9-100550375;