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GeneBe

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.805

Links

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 HGVSp Effect #exon/exons TSL MANE Appris UniProt
CASC19ENST00000642100.1 linkuse as main transcriptn.418-33538G>T intron_variant, non_coding_transcript_variant
PCAT1ENST00000645463.1 linkuse as main transcriptn.855+106053C>A intron_variant, non_coding_transcript_variant
PCAT1ENST00000646670.1 linkuse as main transcriptn.1064+98897C>A intron_variant, non_coding_transcript_variant
PCAT1ENST00000647190.2 linkuse as main transcriptn.1191+63371C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.157
AC:
23857
AN:
152026
Hom.:
4275
Cov.:
32
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.

Other links and lift over

dbSNP: rs16901979; hg19: chr8-128124916;