Genetic Variant PTCSC2:n.165+10767T>A (chr9-97842149-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000649253.2(PTCSC2):n.165+10767T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,244 control chromosomes in the GnomAD database, including 1,296 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 ( 1296 hom., cov: 33)

Consequence

PTCSC2
ENST00000649253.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Publications

2 publications found

Variant links:

Genes affected

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

PTCSC2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.165+10767T>A		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PTCSC2	ENST00000649253.2 link	n.165+10767T>A	intron_variant	Intron 1 of 5
PTCSC2	ENST00000649461.1 link	n.165+10767T>A	intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1 link	n.165+10767T>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18826

AN:

152126

Hom.:

1290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.00769

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.125

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

GnomAD4 genome

AF:

0.124

AC:

18861

AN:

152244

Hom.:

1296

Cov.:

AF XY:

0.127

AC XY:

9418

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.157

AC:

6510

AN:

41536

American (AMR)

AF:

0.134

AC:

2050

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

445

AN:

3466

East Asian (EAS)

AF:

0.00790

AC:

AN:

5192

South Asian (SAS)

AF:

0.112

AC:

543

AN:

4830

European-Finnish (FIN)

AF:

0.184

AC:

1946

AN:

10588

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6883

AN:

68010

Other (OTH)

AF:

0.129

AC:

272

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

833

1667

2500

3334

4167

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0474

Hom.:

Bravo

AF:

0.122

Asia WGS

AF:

0.104

AC:

361

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.0

(source)

DANN

Benign

0.70

PhyloP100

1.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over