Genetic Variant C19orf48P:n.648T>A (chr19-50798809-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000595794.5(C19orf48P):n.648T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

309326

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

163528

African (AFR)

AF:

0.00

AC:

AN:

8664

American (AMR)

AF:

0.00

AC:

AN:

13434

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8462

East Asian (EAS)

AF:

0.00

AC:

AN:

16068

South Asian (SAS)

AF:

0.00

AC:

AN:

42814

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30594

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1364

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

171488

Other (OTH)

AF:

0.00

AC:

AN:

16438

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

(source)

DANN

Benign

0.57

PhyloP100

-0.074

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over