Variant rs4802741 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.824C>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 0.291 in 1,610,044 control chromosomes in the GnomAD database, including 73,222 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 ( 6183 hom., cov: 33)

Exomes 𝑓: 0.29 ( 67039 hom. )

Consequence

C19orf48P
NR_171557.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.218

Variant links:

Genes affected

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

C19orf48P links:

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 (MetaRNN=7.06823E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C19orf48P	NR_171557.1 linkuse as main transcript	n.824C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C19orf48P	ENST00000641539.1 linkuse as main transcript	n.712C>T		non_coding_transcript_exon_variant	1/1
C19orf48P	ENST00000641834.2 linkuse as main transcript	n.1223C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39909

AN:

151998

Hom.:

6176

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

GnomAD3 exomes

AF:

0.304

AC:

75583

AN:

248280

Hom.:

13356

AF XY:

0.308

AC XY:

41325

AN XY:

134054

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.205

Gnomad ASJ exome

AF:

0.224

Gnomad EAS exome

AF:

0.651

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.387

Gnomad NFE exome

AF:

0.282

Gnomad OTH exome

AF:

0.282

GnomAD4 exome

AF:

0.294

AC:

428034

AN:

1457928

Hom.:

67039

Cov.:

AF XY:

0.295

AC XY:

213938

AN XY:

724860

show subpopulations

Gnomad4 AFR exome

AF:

0.142

Gnomad4 AMR exome

AF:

0.207

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.349

Gnomad4 FIN exome

AF:

0.385

Gnomad4 NFE exome

AF:

0.282

Gnomad4 OTH exome

AF:

0.292

GnomAD4 genome

AF:

0.262

AC:

39930

AN:

152116

Hom.:

6183

Cov.:

AF XY:

0.269

AC XY:

19993

AN XY:

74336

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:

0.264

Alfa

AF:

0.272

Hom.:

9671

Bravo

AF:

0.244

TwinsUK

AF:

0.294

AC:

1092

ALSPAC

AF:

0.291

AC:

1120

ESP6500AA

AF:

0.155

AC:

682

ESP6500EA

AF:

0.281

AC:

2414

ExAC

AF:

0.306

AC:

37156

Asia WGS

AF:

0.487

AC:

1689

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.062

BayesDel_addAF

Benign

-0.83

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.3

DANN

Benign

0.51

DEOGEN2

Benign

0.00037

T;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.059

LIST_S2

Benign

0.43

T;.

MetaRNN

Benign

0.0000071

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.34

N;N

MutationTaster

Benign

1.0

P;P

PROVEAN

Benign

-0.62

N;N

REVEL

Benign

0.014

Sift4G

Benign

0.17

T;T

Polyphen

0.0020

B;B

Vest4

0.017

ClinPred

0.000024

GERP RS

0.84

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

Varity_R

0.16

gMVP

0.022

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