Variant chr9-97852835-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+81G>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 0.633 in 152,146 control chromosomes in the GnomAD database, including 30,815 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 ( 30815 hom., cov: 33)

Consequence

PTCSC2
NR_147055.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.794

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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+81G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect
PTCSC2	ENST00000649461.1 linkuse as main transcript	n.165+81G>A	intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000649526.1 linkuse as main transcript	n.165+81G>A	intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000650104.1 linkuse as main transcript	n.165+81G>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

96295

AN:

152030

Hom.:

30788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.663

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.651

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.886

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.630

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

GnomAD4 genome

AF:

0.633

AC:

96358

AN:

152146

Hom.:

30815

Cov.:

AF XY:

0.638

AC XY:

47435

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.662

Gnomad4 AMR

AF:

0.651

Gnomad4 ASJ

AF:

0.479

Gnomad4 EAS

AF:

0.887

Gnomad4 SAS

AF:

0.633

Gnomad4 FIN

AF:

0.640

Gnomad4 NFE

AF:

0.603

Gnomad4 OTH

AF:

0.629

Alfa

AF:

0.618

Hom.:

4240

Bravo

AF:

0.637

Asia WGS

AF:

0.720

AC:

2506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.73

DANN

Benign

0.81

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