Variant rs9991 details in Genebe, Genetics Data Aggregator

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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.302

Variant links:

Genes affected

C19orf48P (HGNC:29667): (chromosome 19 open reading frame 48, pseudogene)

C19orf48P links:

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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
C19orf48P	NR_171557.1 linkuse as main transcript	n.1050C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C19orf48P	ENST00000641834.2 linkuse as main transcript	n.1449C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39922

AN:

152032

Hom.:

6177

Cov.:

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.:

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.:

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.

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