rs9991

Variant summary

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

The NR_171557.1(C19orf48P):​n.1050C>T 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 0.28 in 998,930 control chromosomes in the GnomAD database, including 43,763 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 0.26 ( 6184 hom., cov: 33)
Exomes 𝑓: 0.28 ( 37579 hom. )

Consequence

C19orf48P
NR_171557.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.302
Variant links:
Genes affected
C19orf48P (HGNC:29667): (chromosome 19 open reading frame 48, pseudogene)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C19orf48PNR_171557.1 linkuse as main transcriptn.1050C>T non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
C19orf48PENST00000641834.2 linkuse as main transcriptn.1449C>T non_coding_transcript_exon_variant 4/4

Frequencies

GnomAD3 genomes
AF:
0.263
AC:
39922
AN:
152032
Hom.:
6177
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.255
Gnomad AMR
AF:
0.224
Gnomad ASJ
AF:
0.233
Gnomad EAS
AF:
0.653
Gnomad SAS
AF:
0.381
Gnomad FIN
AF:
0.383
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.255
GnomAD4 exome
AF:
0.284
AC:
240104
AN:
846780
Hom.:
37579
Cov.:
11
AF XY:
0.286
AC XY:
121835
AN XY:
426256
show subpopulations
Gnomad4 AFR exome
AF:
0.136
Gnomad4 AMR exome
AF:
0.206
Gnomad4 ASJ exome
AF:
0.217
Gnomad4 EAS exome
AF:
0.642
Gnomad4 SAS exome
AF:
0.341
Gnomad4 FIN exome
AF:
0.381
Gnomad4 NFE exome
AF:
0.264
Gnomad4 OTH exome
AF:
0.282
GnomAD4 genome
AF:
0.263
AC:
39943
AN:
152150
Hom.:
6184
Cov.:
33
AF XY:
0.269
AC XY:
20005
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.152
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.233
Gnomad4 EAS
AF:
0.653
Gnomad4 SAS
AF:
0.379
Gnomad4 FIN
AF:
0.383
Gnomad4 NFE
AF:
0.284
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.269
Hom.:
7698
Bravo
AF:
0.244
Asia WGS
AF:
0.488
AC:
1691
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.7
DANN
Benign
0.43
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs9991; hg19: chr19-51301230; COSMIC: COSV54517312; COSMIC: COSV54517312; API