Genetic Variant ENST00000430058.2:n.331-11449G>A (chr9-97734383-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430058.2(PTCSC2):n.331-11449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,858 control chromosomes in the GnomAD database, including 11,289 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 0.38 ( 11289 hom., cov: 32)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.778-9853G>A		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PTCSC2	ENST00000430058.2 link	n.331-11449G>A	intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1 link	n.471-9853G>A	intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1 link	n.331-9853G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

57093

AN:

151740

Hom.:

11269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.352

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.0461

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.437

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.427

Gnomad OTH

AF:

0.349

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

GnomAD4 genome

AF:

0.376

AC:

57154

AN:

151858

Hom.:

11289

Cov.:

AF XY:

0.372

AC XY:

27623

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.352

AC:

14588

AN:

41416

American (AMR)

AF:

0.355

AC:

5415

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.289

AC:

1003

AN:

3468

East Asian (EAS)

AF:

0.0460

AC:

238

AN:

5178

South Asian (SAS)

AF:

0.262

AC:

1261

AN:

4810

European-Finnish (FIN)

AF:

0.437

AC:

4600

AN:

10520

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.427

AC:

28961

AN:

67894

Other (OTH)

AF:

0.349

AC:

735

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1846

3693

5539

7386

9232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.399

Hom.:

5189

Bravo

AF:

0.369

Asia WGS

AF:

0.190

AC:

661

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.9

(source)

DANN

Benign

0.70

PhyloP100

0.031

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