Variant 9-97853077-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NR_147055.1(PTCSC2):n.4G>A 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 0.817 in 152,152 control chromosomes in the GnomAD database, including 51,483 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.82 ( 51483 hom., cov: 32)

Consequence

PTCSC2
NR_147055.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.485

Variant links:

Genes affected

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

PTCSC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 9-97853077-C-T is Benign according to our data. Variant chr9-97853077-C-T is described in ClinVar as [Benign]. Clinvar id is 1250293.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.4G>A		non_coding_transcript_exon_variant	1/11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
PTCSC2	ENST00000649461.1 link	n.4G>A	non_coding_transcript_exon_variant	1/11
PTCSC2	ENST00000649526.1 link	n.4G>A	non_coding_transcript_exon_variant	1/3
PTCSC2	ENST00000650104.1 link	n.4G>A	non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes

AF:

0.816

AC:

124137

AN:

152036

Hom.:

51424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.943

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.820

Gnomad ASJ

AF:

0.763

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.801

Gnomad FIN

AF:

0.831

Gnomad MID

AF:

0.812

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.821

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

GnomAD4 genome

AF:

0.817

AC:

124248

AN:

152152

Hom.:

51483

Cov.:

AF XY:

0.823

AC XY:

61245

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.943

Gnomad4 AMR

AF:

0.821

Gnomad4 ASJ

AF:

0.763

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.800

Gnomad4 FIN

AF:

0.831

Gnomad4 NFE

AF:

0.730

Gnomad4 OTH

AF:

0.823

Alfa

AF:

0.767

Hom.:

5307

Bravo

AF:

0.825

Asia WGS

AF:

0.917

AC:

3179

AN:

3466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.9

DANN

Benign

0.94

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over