dbSNP rs1043315: C19orf48P:n.560C>T (chr19-50798897-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000595794.5(C19orf48P):n.560C>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 0.293 in 402,388 control chromosomes in the GnomAD database, including 19,420 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 0.27 ( 6408 hom., cov: 33)

Exomes 𝑓: 0.31 ( 13012 hom. )

Consequence

C19orf48P
ENST00000595794.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69

Variant links:

Genes affected

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
C19orf48P	NR_171554.1 link	n.351C>T	non_coding_transcript_exon_variant	Exon 5 of 5
C19orf48P	NR_171555.1 link	n.190C>T	non_coding_transcript_exon_variant	Exon 4 of 4
C19orf48P	NR_171556.1 link	n.695C>T	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C19orf48P	ENST00000595794.5 link	n.560C>T	non_coding_transcript_exon_variant	Exon 3 of 3	1
C19orf48P	ENST00000598463.5 link	n.651C>T	non_coding_transcript_exon_variant	Exon 5 of 5	1
C19orf48P	ENST00000593287.5 link	n.526C>T	non_coding_transcript_exon_variant	Exon 3 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41231

AN:

151938

Hom.:

6400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.256

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.233

Gnomad EAS

AF:

0.652

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.383

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.262

GnomAD4 exome

AF:

0.307

AC:

76833

AN:

250332

Hom.:

13012

Cov.:

AF XY:

0.313

AC XY:

42552

AN XY:

136052

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.208

Gnomad4 ASJ exome

AF:

0.221

Gnomad4 EAS exome

AF:

0.644

Gnomad4 SAS exome

AF:

0.348

Gnomad4 FIN exome

AF:

0.383

Gnomad4 NFE exome

AF:

0.282

Gnomad4 OTH exome

AF:

0.299

GnomAD4 genome

AF:

0.271

AC:

41255

AN:

152056

Hom.:

6408

Cov.:

AF XY:

0.277

AC XY:

20604

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.182

Gnomad4 AMR

AF:

0.228

Gnomad4 ASJ

AF:

0.233

Gnomad4 EAS

AF:

0.652

Gnomad4 SAS

AF:

0.379

Gnomad4 FIN

AF:

0.383

Gnomad4 NFE

AF:

0.284

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.263

Hom.:

1940

Bravo

AF:

0.254

Asia WGS

AF:

0.490

AC:

1702

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.90

DANN

Benign

0.55

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over