rs7850258

Variant names:

• chr9-97786731-A-G
• rs7850258
• ENST00000430058.2:n.330+19109T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-97786731-A-G
• chr9-97786731-A-T

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.330+19109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,026 control chromosomes in the GnomAD database, including 39,829 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 (39829 hom., cov: 31)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1	n.777+17520T>C		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC2	ENST00000430058.2	n.330+19109T>C		intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1	n.470+17520T>C		intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1	n.330+19109T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109300 AN: 151908 Hom.: 39802 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.719 AC: 109380 AN: 152026 Hom.: 39829 Cov.: 31 AF XY: 0.723 AC XY: 53736 AN XY: 74306

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.719

Alfa AF: 0.678 Hom.: 77222

Bravo AF: 0.727

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7850258; hg19: chr9-100549013;