rs894673

chr9-97849988-A-T

Variant summary

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

The NR_147055.1(PTCSC2):n.165+2928T>A 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 0.633 in 152,112 control chromosomes in the GnomAD database, including 30,739 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 (30739 hom., cov: 32)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.165+2928T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.165+2928T>A		intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000649526.1	n.165+2928T>A		intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000650104.1	n.165+2928T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96197 AN: 151996 Hom.: 30712 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.633 AC: 96261 AN: 152112 Hom.: 30739 Cov.: 32 AF XY: 0.637 AC XY: 47385 AN XY: 74366

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.628

Alfa AF: 0.620 Hom.: 3647

Bravo AF: 0.637

Asia WGS AF: 0.720 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	11
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs894673; hg19: chr9-100612270;