9-97788093-T-A

Variant names:

• chr9-97788093-T-A
• rs7030241
• ENST00000824829.1:n.809T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000824829.1(ENSG00000307267):​n.809T>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 0.719 in 152,004 control chromosomes in the GnomAD database, including 39,826 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 0.72 (39826 hom., cov: 30)
• Consequence: ENSG00000307267 ENST00000824829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 4 publications found

Genes affected

ENSG00000307267 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1	n.777+16158A>T		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307267	ENST00000824829.1	n.809T>A		non_coding_transcript_exon_variant	Exon 2 of 2
PTCSC2	ENST00000430058.2	n.330+17747A>T		intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1	n.470+16158A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109277 AN: 151886 Hom.: 39799 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.719 AC: 109357 AN: 152004 Hom.: 39826 Cov.: 30 AF XY: 0.723 AC XY: 53723 AN XY: 74288

African (AFR) AF: 0.812 AC: 33652 AN: 41466

American (AMR) AF: 0.709 AC: 10830 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2350 AN: 3468

East Asian (EAS) AF: 0.891 AC: 4602 AN: 5164

South Asian (SAS) AF: 0.772 AC: 3719 AN: 4816

European-Finnish (FIN) AF: 0.669 AC: 7076 AN: 10570

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44968 AN: 67934

Other (OTH) AF: 0.718 AC: 1514 AN: 2108

Alfa AF: 0.591 Hom.: 1777

Bravo AF: 0.727

Asia WGS AF: 0.803 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.30
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7030241; hg19: chr9-100550375;