19-50798138-C-G

Variant names:

• chr19-50798138-C-G
• rs4801853
• ENST00000598463.5:n.1410G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000598463.5(C19orf48P):​n.1410G>C 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 0.00000642 in 1,401,094 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000064 (0 hom.)
• Consequence: C19orf48P ENST00000598463.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08719069).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C19orf48P	NR_171554.1	n.1110G>C		non_coding_transcript_exon_variant	Exon 5 of 5
C19orf48P	NR_171555.1	n.949G>C		non_coding_transcript_exon_variant	Exon 4 of 4
C19orf48P	NR_171556.1	n.1454G>C		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C19orf48P	ENST00000598463.5	n.1410G>C		non_coding_transcript_exon_variant	Exon 5 of 5	1
C19orf48P	ENST00000596287.6	n.916G>C		non_coding_transcript_exon_variant	Exon 4 of 4	2
C19orf48P	ENST00000596655.1	n.1262G>C		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000642 AC: 9 AN: 1401094 Hom.: 0 Cov.: 34 AF XY: 0.0000101 AC XY: 7 AN XY: 689760

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000833

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.28
DANN	Benign	0.68
DEOGEN2	Benign	0.022	T;T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.042	N
LIST_S2	Benign	0.34	T;.
M_CAP	Benign	0.0044	T
MetaRNN	Benign	0.087	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N;N
PROVEAN	Uncertain	-4.3	D;D
REVEL	Benign	0.0090
Sift4G	Pathogenic	0.0	D;D
Polyphen		0.11	B;B
Vest4		0.15
MutPred		0.21		Gain of helix (P = 0.0078);Gain of helix (P = 0.0078);
MVP		0.45
ClinPred		0.088	T
GERP RS		-2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.32
gMVP		0.026

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

Other links and lift over

dbSNP: rs4801853; hg19: chr19-51301395;