chr19-50798199-G-C

Variant names:

• chr19-50798199-G-C
• rs4802741
• ENST00000598463.5:n.1349C>G

Variant summary

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

The ENST00000598463.5(C19orf48P):​n.1349C>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 ENST00000598463.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 36 publications found

Genes affected

C19orf48P (HGNC:):

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

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 (MetaRNN=0.058652163).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	NR_171554.1		n.1049C>G		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	NR_171555.1		n.888C>G		non_coding_transcript_exon	Exon 4 of 4
	C19orf48P	NR_171556.1		n.1393C>G		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	ENST00000598463.5	TSL:1	n.1349C>G		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	ENST00000596287.7	TSL:2	n.919C>G		non_coding_transcript_exon	Exon 4 of 4
	C19orf48P	ENST00000596655.1	TSL:2	n.1201C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 16220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.63
DANN	Benign	0.33
DEOGEN2	Benign	0.025	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.075	N
LIST_S2	Benign	0.31	T
M_CAP	Benign	0.0039	T
MetaRNN	Benign	0.059	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.34	N
PhyloP100		-0.22
PROVEAN	Uncertain	-3.1	D
REVEL	Benign	0.041
Sift4G	Benign	0.37	T
Polyphen		0.097	B
Vest4		0.037
MutPred		0.33		Loss of stability (P = 0.0142)
MVP		0.13
ClinPred		0.13	T
GERP RS		0.84
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0
Varity_R		0.35
gMVP		0.031

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: rs4802741; hg19: chr19-51301456;