rs10983893

Variant names:

• chr9-97833883-T-C
• rs10983893
• ENST00000649461.1:n.165+19033A>G

Variant summary

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

The NR_147055.1(PTCSC2):​n.165+19033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,264 control chromosomes in the GnomAD database, including 1,321 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 0.12 (1321 hom., cov: 33)
• Consequence: PTCSC2 NR_147055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

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 (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1	n.165+19033A>G		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC2	ENST00000649461.1	n.165+19033A>G		intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1	n.165+19033A>G		intron_variant	Intron 1 of 2
PTCSC2	ENST00000650104.1	n.165+19033A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18967 AN: 152146 Hom.: 1313 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.00771

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.125 AC: 19008 AN: 152264 Hom.: 1321 Cov.: 33 AF XY: 0.128 AC XY: 9498 AN XY: 74444

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.00792

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.129

Alfa AF: 0.108 Hom.: 1316

Bravo AF: 0.123

Asia WGS AF: 0.105 AC: 365 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	6.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10983893; hg19: chr9-100596165;