Genetic Variant ENST00000598463.5:n.1410G>A (chr19-50798138-C-T) – 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.1410G>A 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 1,552,884 control chromosomes in the GnomAD database, including 70,653 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 ( 6168 hom., cov: 32)

Exomes 𝑓: 0.29 ( 64485 hom. )

Consequence

C19orf48P
ENST00000598463.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.404

Publications

42 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=1.2199035E-5).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598463.5. 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.1110G>A	non_coding_transcript_exon	Exon 5 of 5
C19orf48P	NR_171555.1	n.949G>A	non_coding_transcript_exon	Exon 4 of 4
C19orf48P	NR_171556.1	n.1454G>A	non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
C19orf48P	ENST00000598463.5	TSL:1	n.1410G>A	non_coding_transcript_exon	Exon 5 of 5
C19orf48P	ENST00000596287.7	TSL:2	n.980G>A	non_coding_transcript_exon	Exon 4 of 4
C19orf48P	ENST00000596655.1	TSL:2	n.1262G>A	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39875

AN:

151976

Hom.:

6161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.254

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:

0.254

GnomAD2 exomes

AF:

0.306

AC:

63016

AN:

205822

AF XY:

0.309

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.203

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.650

Gnomad FIN exome

AF:

0.384

Gnomad NFE exome

AF:

0.281

Gnomad OTH exome

AF:

0.290

GnomAD4 exome

AF:

0.294

AC:

411297

AN:

1400790

Hom.:

64485

Cov.:

AF XY:

0.295

AC XY:

203275

AN XY:

689568

show subpopulations

African (AFR)

AF:

0.141

AC:

4501

AN:

31922

American (AMR)

AF:

0.205

AC:

7729

AN:

37726

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

4860

AN:

21906

East Asian (EAS)

AF:

0.645

AC:

25211

AN:

39080

South Asian (SAS)

AF:

0.349

AC:

26587

AN:

76180

European-Finnish (FIN)

AF:

0.384

AC:

19524

AN:

50898

Middle Eastern (MID)

AF:

0.218

AC:

1185

AN:

5448

European-Non Finnish (NFE)

AF:

0.282

AC:

304851

AN:

1079988

Other (OTH)

AF:

0.292

AC:

16849

AN:

57642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

17363

34726

52090

69453

86816

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10528

21056

31584

42112

52640

<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:

39896

AN:

152094

Hom.:

6168

Cov.:

AF XY:

0.269

AC XY:

19974

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.152

AC:

6307

AN:

41526

American (AMR)

AF:

0.224

AC:

3417

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

810

AN:

3472

East Asian (EAS)

AF:

0.653

AC:

3363

AN:

5154

South Asian (SAS)

AF:

0.379

AC:

1825

AN:

4820

European-Finnish (FIN)

AF:

0.383

AC:

4046

AN:

10574

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19285

AN:

67948

Other (OTH)

AF:

0.262

AC:

554

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1437

2874

4311

5748

7185

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:

0.272

Hom.:

19313

Bravo

AF:

0.244

TwinsUK

AF:

0.294

AC:

1092

ALSPAC

AF:

0.291

AC:

1120

ESP6500AA

AF:

0.154

AC:

680

ESP6500EA

AF:

0.281

AC:

2413

ExAC

AF:

0.299

AC:

36036

Asia WGS

AF:

0.488

AC:

1691

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.89

(source)

DANN

Benign

0.75

DEOGEN2

Benign

0.023

Eigen

Benign

-0.96

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.056

LIST_S2

Benign

0.29

MetaRNN

Benign

0.000012

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.0

PhyloP100

-0.40

PROVEAN

Pathogenic

-5.4

REVEL

Benign

0.098

Sift4G

Pathogenic

0.0

Polyphen

0.97

Vest4

0.079

ClinPred

0.052

GERP RS

-2.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.32

gMVP

0.034

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over