9-97845215-A-G

Variant names:

• chr9-97845215-A-G
• rs6478437
• ENST00000824745.1:n.465T>C

Variant summary

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

The ENST00000824745.1(PTCSC2):​n.465T>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 0.633 in 152,144 control chromosomes in the GnomAD database, including 30,773 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 (30773 hom., cov: 34)
• Consequence: PTCSC2 ENST00000824745.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 2 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824745.1. 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+7701T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000824745.1		n.465T>C		non_coding_transcript_exon	Exon 2 of 2
	PTCSC2	ENST00000824746.1		n.494T>C		non_coding_transcript_exon	Exon 2 of 2
	PTCSC2	ENST00000649253.2		n.165+7701T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96245 AN: 152026 Hom.: 30746 Cov.: 34

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.602

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: 96309 AN: 152144 Hom.: 30773 Cov.: 34 AF XY: 0.637 AC XY: 47405 AN XY: 74368

African (AFR) AF: 0.662 AC: 27444 AN: 41462

American (AMR) AF: 0.652 AC: 9966 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4595 AN: 5186

South Asian (SAS) AF: 0.633 AC: 3054 AN: 4826

European-Finnish (FIN) AF: 0.640 AC: 6770 AN: 10578

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40939 AN: 68010

Other (OTH) AF: 0.629 AC: 1329 AN: 2114

Alfa AF: 0.622 Hom.: 5984

Bravo AF: 0.637

Asia WGS AF: 0.720 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6478437;

hg19: chr9-100607497;