rs3758249

Variant names:

• chr9-97851858-T-C
• rs3758249
• ENST00000649253.2:n.165+1058A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147055.1(PTCSC2):​n.165+1058A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 148,154 control chromosomes in the GnomAD database, including 29,676 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 0.63 (29676 hom., cov: 23)
• Consequence: PTCSC2 NR_147055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 39 publications found

Genes affected

PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_147055.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.165+1058A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000649253.2		n.165+1058A>G		intron	N/A
	PTCSC2	ENST00000649461.1		n.165+1058A>G		intron	N/A
	PTCSC2	ENST00000649526.1		n.165+1058A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 93191 AN: 148036 Hom.: 29650 Cov.: 23

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.629 AC: 93253 AN: 148154 Hom.: 29676 Cov.: 23 AF XY: 0.633 AC XY: 45603 AN XY: 72030

African (AFR) AF: 0.657 AC: 26171 AN: 39862

American (AMR) AF: 0.649 AC: 9629 AN: 14848

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1654 AN: 3452

East Asian (EAS) AF: 0.885 AC: 4293 AN: 4850

South Asian (SAS) AF: 0.629 AC: 2942 AN: 4674

European-Finnish (FIN) AF: 0.629 AC: 6190 AN: 9838

Middle Eastern (MID) AF: 0.610 AC: 177 AN: 290

European-Non Finnish (NFE) AF: 0.602 AC: 40557 AN: 67404

Other (OTH) AF: 0.627 AC: 1276 AN: 2034

Alfa AF: 0.619 Hom.: 3645

Bravo AF: 0.637

Asia WGS AF: 0.719 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.31
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs3758249; hg19: chr9-100614140;