rs892416

Positions:

• chr15-69667454-C-A
• chr15-69667454-C-G
• chr15-69667454-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_126437.1(PCAT29):​n.370-10092C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.026 (148 hom., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: PCAT29 NR_126437.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

PCAT29 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCAT29	NR_126437.1	n.370-10092C>A		intron_variant, non_coding_transcript_variant
PCAT29	NR_126438.1	n.115-4286C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRAIC	ENST00000646247.2	n.1911-10092C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2172 AN: 81988 Hom.: 149 Cov.: 17 FAILED QC

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.0675

Gnomad AMR AF: 0.00881

Gnomad ASJ AF: 0.0209

Gnomad EAS AF: 0.00574

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.00381

Gnomad MID AF: 0.0333

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0253

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0265 AC: 2173 AN: 82084 Hom.: 148 Cov.: 17 AF XY: 0.0246 AC XY: 1008 AN XY: 41048

Gnomad4 AFR AF: 0.0498

Gnomad4 AMR AF: 0.00889

Gnomad4 ASJ AF: 0.0209

Gnomad4 EAS AF: 0.00575

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.00381

Gnomad4 NFE AF: 0.0172

Gnomad4 OTH AF: 0.0250

Alfa AF: 0.00157 Hom.: 6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs892416; hg19: chr15-69959793; COSMIC: COSV73740768;