rs16901979

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000642100(CASC19):n.418-33538G>T 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 0.157 in 152026 control chromosomes in the gnomAD Genomes database, including 4275 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 0.16 ( 4275 hom., cov: 32)

Consequence

CASC19
ENST00000642100 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.805

Links

CASC19 (HGNC:49476):

PCAT1 (HGNC:43022):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
CASC19	ENST00000642100.1 linkuse as main transcript	n.418-33538G>T	intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1 linkuse as main transcript	n.855+106053C>A	intron_variant, non_coding_transcript_variant
PCAT1	ENST00000646670.1 linkuse as main transcript	n.1064+98897C>A	intron_variant, non_coding_transcript_variant
PCAT1	ENST00000647190.2 linkuse as main transcript	n.1191+63371C>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23857

AN:

152026

Hom.:

4275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.434

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0684

Gnomad ASJ

AF:

0.0389

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0507

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0322

Gnomad OTH

AF:

0.112

Alfa

AF:

0.0660

Hom.:

1086

Bravo

AF:

0.170

Asia WGS

AF:

0.146

AC:

508

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

Cadd

Benign

0.12

Dann

Benign

0.21

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over