dbSNP rs4802741: C19orf48P:n.1349C>T (chr19-50798199-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000598463.5(C19orf48P):n.1349C>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
ENST00000598463.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.218

Publications

36 publications found

Variant links:

Genes affected

C19orf48P (HGNC:):

C19orf48P links:

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

C19orf48P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank
C19orf48P	NR_171554.1 link	n.1049C>T	non_coding_transcript_exon_variant	Exon 5 of 5
C19orf48P	NR_171555.1 link	n.888C>T	non_coding_transcript_exon_variant	Exon 4 of 4
C19orf48P	NR_171556.1 link	n.1393C>T	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C19orf48P	ENST00000598463.5 link	n.1349C>T	non_coding_transcript_exon_variant	Exon 5 of 5	1
C19orf48P	ENST00000596287.7 link	n.919C>T	non_coding_transcript_exon_variant	Exon 4 of 4	2
C19orf48P	ENST00000596655.1 link	n.1201C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2

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

GnomAD2 exomes

AF:

0.304

AC:

75583

AN:

248280

AF XY:

0.308

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 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

African (AFR)

AF:

0.142

AC:

4764

AN:

33436

American (AMR)

AF:

0.207

AC:

9218

AN:

44526

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

5766

AN:

25848

East Asian (EAS)

AF:

0.645

AC:

25576

AN:

39632

South Asian (SAS)

AF:

0.349

AC:

29961

AN:

85770

European-Finnish (FIN)

AF:

0.385

AC:

20483

AN:

53174

Middle Eastern (MID)

AF:

0.218

AC:

1250

AN:

5740

European-Non Finnish (NFE)

AF:

0.282

AC:

313429

AN:

1109606

Other (OTH)

AF:

0.292

AC:

17587

AN:

60196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

18635

37270

55905

74540

93175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10568

21136

31704

42272

52840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.262

AC:

39930

AN:

152116

Hom.:

6183

Cov.:

AF XY:

0.269

AC XY:

19993

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.152

AC:

6312

AN:

41528

American (AMR)

AF:

0.224

AC:

3417

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

810

AN:

3472

East Asian (EAS)

AF:

0.653

AC:

3363

AN:

5152

South Asian (SAS)

AF:

0.379

AC:

1825

AN:

4818

European-Finnish (FIN)

AF:

0.383

AC:

4053

AN:

10580

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19303

AN:

67962

Other (OTH)

AF:

0.264

AC:

556

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1447

2895

4342

5790

7237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

418

836

1254

1672

2090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.274

Hom.:

16220

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

(source)

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

PhyloP100

-0.22

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

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over