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

new If you want to explore the variant's impact on the transcript ENST00000595794.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595794.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
C19orf48P	ENST00000595794.5	TSL:1	n.648T>C	non_coding_transcript_exon	Exon 3 of 3
C19orf48P	ENST00000598463.5	TSL:1	n.739T>C	non_coding_transcript_exon	Exon 5 of 5
C19orf48P	ENST00000596287.7	TSL:2	n.309T>C	non_coding_transcript_exon	Exon 4 of 4

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over