dbSNP rs9991: C19orf48P:n.1575C>T (chr19-50797973-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.1575C>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
ENST00000598463.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.302

Publications

30 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 (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	Effect	Exon rank
C19orf48P	NR_171554.1 link	n.1275C>T	non_coding_transcript_exon_variant	Exon 5 of 5
C19orf48P	NR_171555.1 link	n.1114C>T	non_coding_transcript_exon_variant	Exon 4 of 4
C19orf48P	NR_171556.1 link	n.1619C>T	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C19orf48P	ENST00000598463.5 link	n.1575C>T	non_coding_transcript_exon_variant	Exon 5 of 5	1
C19orf48P	ENST00000596287.7 link	n.1145C>T	non_coding_transcript_exon_variant	Exon 4 of 4	2
C19orf48P	ENST00000596655.1 link	n.1427C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2

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

African (AFR)

AF:

0.136

AC:

2793

AN:

20566

American (AMR)

AF:

0.206

AC:

4798

AN:

23290

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

3471

AN:

15970

East Asian (EAS)

AF:

0.642

AC:

21810

AN:

33994

South Asian (SAS)

AF:

0.341

AC:

16204

AN:

47512

European-Finnish (FIN)

AF:

0.381

AC:

13035

AN:

34176

Middle Eastern (MID)

AF:

0.200

AC:

531

AN:

2654

European-Non Finnish (NFE)

AF:

0.264

AC:

166593

AN:

630042

Other (OTH)

AF:

0.282

AC:

10869

AN:

38576

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

7914

15829

23743

31658

39572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4760

9520

14280

19040

23800

<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:

39943

AN:

152150

Hom.:

6184

Cov.:

AF XY:

0.269

AC XY:

20005

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.152

AC:

6319

AN:

41516

American (AMR)

AF:

0.224

AC:

3419

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

810

AN:

3470

East Asian (EAS)

AF:

0.653

AC:

3366

AN:

5152

South Asian (SAS)

AF:

0.379

AC:

1827

AN:

4822

European-Finnish (FIN)

AF:

0.383

AC:

4058

AN:

10592

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19297

AN:

67986

Other (OTH)

AF:

0.263

AC:

556

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1466

2933

4399

5866

7332

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:

0.265

Hom.:

9504

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

(source)

DANN

Benign

0.43

PhyloP100

-0.30

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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