Variant rs892416 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Variant links:

Genes affected

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

DRAIC links:

PCAT29 (HGNC:):

PCAT29 links:

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ACMG classification

Classification made for transcript

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 linkuse as main transcript	n.370-10092C>A		intron_variant, non_coding_transcript_variant
PCAT29	NR_126438.1 linkuse as main transcript	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 linkuse as main transcript	n.1911-10092C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

2172

AN:

81988

Hom.:

149

Cov.:

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.:

AF XY:

0.0246

AC XY:

1008

AN XY:

41048

show subpopulations

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.:

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

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