ENST00000824829.1:n.462T>C

Variant names:

• chr9-97787746-T-C
• rs1443438
• ENST00000824829.1:n.462T>C

Variant summary

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

The ENST00000824829.1(ENSG00000307267):​n.462T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 151,998 control chromosomes in the GnomAD database, including 39,870 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 (39870 hom., cov: 30)
• Consequence: ENSG00000307267 ENST00000824829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 23 publications found

Genes affected

ENSG00000307267 (HGNC:):

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824829.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.777+16505A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307267	ENST00000824829.1		n.462T>C		non_coding_transcript_exon	Exon 2 of 2
	PTCSC2	ENST00000430058.2	TSL:2	n.330+18094A>G		intron	N/A
	PTCSC2	ENST00000648027.1		n.470+16505A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109322 AN: 151880 Hom.: 39840 Cov.: 30

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.890

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: 0.720 AC: 109408 AN: 151998 Hom.: 39870 Cov.: 30 AF XY: 0.724 AC XY: 53756 AN XY: 74272

African (AFR) AF: 0.813 AC: 33703 AN: 41456

American (AMR) AF: 0.709 AC: 10833 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4593 AN: 5160

South Asian (SAS) AF: 0.772 AC: 3710 AN: 4806

European-Finnish (FIN) AF: 0.669 AC: 7067 AN: 10560

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44986 AN: 67954

Other (OTH) AF: 0.718 AC: 1516 AN: 2110

Alfa AF: 0.684 Hom.: 132419

Bravo AF: 0.728

Asia WGS AF: 0.803 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.9
DANN	Benign	0.58
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs1443438; hg19: chr9-100550028;