chr19-50798897-G-C

Variant names:

• chr19-50798897-G-C
• rs1043315
• ENST00000595794.5:n.560C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000595794.5(C19orf48P):​n.560C>G 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)
• Consequence: C19orf48P ENST00000595794.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 13 publications found

Genes affected

C19orf48P (HGNC:):

C19orf48P (HGNC:29667): (chromosome 19 open reading frame 48, pseudogene)

SNORD88B (HGNC:32748): (small nucleolar RNA, C/D box 88B)

ACMG classification

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=-0.84).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	NR_171554.1		n.351C>G		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	NR_171555.1		n.190C>G		non_coding_transcript_exon	Exon 4 of 4
	C19orf48P	NR_171556.1		n.695C>G		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	ENST00000595794.5	TSL:1	n.560C>G		non_coding_transcript_exon	Exon 3 of 3
	C19orf48P	ENST00000598463.5	TSL:1	n.651C>G		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	ENST00000593287.5	TSL:5	n.526C>G		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.32
DANN	Benign	0.43
PhyloP100		-1.7

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

Other links and lift over

dbSNP: rs1043315; hg19: chr19-51302154;