Variant 9-97834709-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_147055.1(PTCSC2):n.165+18207G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,196 control chromosomes in the GnomAD database, including 1,859 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 0.11 ( 1859 hom., cov: 32)

Consequence

PTCSC2
NR_147055.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

Variant links:

Genes affected

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

PTCSC2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCSC2	NR_147055.1 linkuse as main transcript	n.165+18207G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect
PTCSC2	ENST00000649461.1 linkuse as main transcript	n.165+18207G>A	intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000649526.1 linkuse as main transcript	n.165+18207G>A	intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000650104.1 linkuse as main transcript	n.165+18207G>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16709

AN:

152076

Hom.:

1848

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.0806

Gnomad EAS

AF:

0.603

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.105

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

GnomAD4 genome

AF:

0.110

AC:

16730

AN:

152196

Hom.:

1859

Cov.:

AF XY:

0.116

AC XY:

8663

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0243

Gnomad4 AMR

AF:

0.185

Gnomad4 ASJ

AF:

0.0806

Gnomad4 EAS

AF:

0.604

Gnomad4 SAS

AF:

0.125

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.128

Hom.:

495

Bravo

AF:

0.110

Asia WGS

AF:

0.311

AC:

1079

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.93

DANN

Benign

0.17

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over