Genetic Variant C19orf48P:n.648T>C (chr19-50798809-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000595794.5(C19orf48P):n.648T>C 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 0.293 in 460,806 control chromosomes in the GnomAD database, including 22,691 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 ( 6186 hom., cov: 33)

Exomes 𝑓: 0.31 ( 16505 hom. )

Consequence

C19orf48P
ENST00000595794.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0740

Publications

21 publications found

Variant links:

Genes affected

C19orf48P (HGNC:):

C19orf48P links:

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

C19orf48P links:

SNORD88B (HGNC:32748): (small nucleolar RNA, C/D box 88B)

SNORD88B 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 (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
C19orf48P	NR_171554.1 link	n.439T>C	non_coding_transcript_exon_variant	Exon 5 of 5
C19orf48P	NR_171555.1 link	n.278T>C	non_coding_transcript_exon_variant	Exon 4 of 4
C19orf48P	NR_171556.1 link	n.783T>C	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C19orf48P	ENST00000595794.5 link	n.648T>C	non_coding_transcript_exon_variant	Exon 3 of 3	1
C19orf48P	ENST00000598463.5 link	n.739T>C	non_coding_transcript_exon_variant	Exon 5 of 5	1
C19orf48P	ENST00000596287.7 link	n.309T>C	non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39955

AN:

151988

Hom.:

6178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

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:

0.256

GnomAD4 exome

AF:

0.308

AC:

95122

AN:

308700

Hom.:

16505

Cov.:

AF XY:

0.311

AC XY:

50794

AN XY:

163174

show subpopulations

African (AFR)

AF:

0.144

AC:

1244

AN:

8648

American (AMR)

AF:

0.205

AC:

2755

AN:

13416

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

1871

AN:

8454

East Asian (EAS)

AF:

0.645

AC:

10317

AN:

15994

South Asian (SAS)

AF:

0.346

AC:

14802

AN:

42730

European-Finnish (FIN)

AF:

0.381

AC:

11635

AN:

30554

Middle Eastern (MID)

AF:

0.218

AC:

297

AN:

1360

European-Non Finnish (NFE)

AF:

0.277

AC:

47399

AN:

171130

Other (OTH)

AF:

0.293

AC:

4802

AN:

16414

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3019

6038

9058

12077

15096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

372

744

1116

1488

1860

<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:

0.263

AC:

39977

AN:

152106

Hom.:

6186

Cov.:

AF XY:

0.269

AC XY:

20012

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.153

AC:

6370

AN:

41500

American (AMR)

AF:

0.223

AC:

3416

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

810

AN:

3472

East Asian (EAS)

AF:

0.653

AC:

3371

AN:

5160

South Asian (SAS)

AF:

0.379

AC:

1831

AN:

4828

European-Finnish (FIN)

AF:

0.383

AC:

4048

AN:

10580

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19284

AN:

67964

Other (OTH)

AF:

0.264

AC:

556

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1479

2958

4437

5916

7395

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:

0.264

Hom.:

16186

Bravo

AF:

0.245

Asia WGS

AF:

0.488

AC:

1692

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.0

(source)

DANN

Benign

0.34

PhyloP100

-0.074

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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