13-23889479-C-G

Position:

• chr13-23889479-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_172511.1(PCOTH):​n.14C>G 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 0.246 in 569,184 control chromosomes in the GnomAD database, including 17,959 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.24 (4576 hom., cov: 32)
  • Exomes 𝑓: 0.25 (13383 hom.)
• Consequence: PCOTH NR_172511.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.274

Genes affected

PCOTH (HGNC:39839): (prostate and testis expressed opposite C1QTNF9B and MIPEP) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 13-23889479-C-G is Benign according to our data. Variant chr13-23889479-C-G is described in ClinVar as [Benign]. Clinvar id is 1276392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCOTH	NR_172511.1	n.14C>G		non_coding_transcript_exon_variant	1/4
PCOTH	NR_172512.1	n.14C>G		non_coding_transcript_exon_variant	1/4
PCOTH	NR_172513.1	n.14C>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCOTH	ENST00000382133.9	n.170+468C>G		intron_variant		1
PCOTH	ENST00000663394.1	n.49C>G		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36631 AN: 152020 Hom.: 4580 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.248

GnomAD4 exome AF: 0.247 AC: 103120 AN: 417044 Hom.: 13383 AF XY: 0.246 AC XY: 50898 AN XY: 206696

Gnomad4 AFR exome AF: 0.198

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.265

Gnomad4 EAS exome AF: 0.396

Gnomad4 SAS exome AF: 0.112

Gnomad4 FIN exome AF: 0.305

Gnomad4 NFE exome AF: 0.236

Gnomad4 OTH exome AF: 0.243

GnomAD4 genome AF: 0.241 AC: 36633 AN: 152140 Hom.: 4576 Cov.: 32 AF XY: 0.242 AC XY: 18027 AN XY: 74388

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.245

Alfa AF: 0.230 Hom.: 497

Bravo AF: 0.240

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	9.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077440; hg19: chr13-24463618;