19-50798945-T-C

Variant names:

• chr19-50798945-T-C
• rs3745526
• ENST00000595794.5:n.512A>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.512A>G 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 0.0000398 in 452,100 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: 𝑓 0.000059 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000030 (0 hom.)
• Consequence: C19orf48P ENST00000595794.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 21 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=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C19orf48P	NR_171554.1	n.303A>G		non_coding_transcript_exon_variant	Exon 5 of 5
C19orf48P	NR_171555.1	n.142A>G		non_coding_transcript_exon_variant	Exon 4 of 4
C19orf48P	NR_171556.1	n.647A>G		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C19orf48P	ENST00000595794.5	n.512A>G		non_coding_transcript_exon_variant	Exon 3 of 3	1
C19orf48P	ENST00000598463.5	n.603A>G		non_coding_transcript_exon_variant	Exon 5 of 5	1
C19orf48P	ENST00000593287.5	n.478A>G		non_coding_transcript_exon_variant	Exon 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0000593 AC: 9 AN: 151744 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000726

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000736

Gnomad OTH AF: 0.000480

GnomAD4 exome AF: 0.0000300 AC: 9 AN: 300238 Hom.: 0 Cov.: 0 AF XY: 0.0000237 AC XY: 4 AN XY: 168432

African (AFR) AF: 0.00 AC: 0 AN: 8352

American (AMR) AF: 0.0000398 AC: 1 AN: 25136

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9500

East Asian (EAS) AF: 0.00 AC: 0 AN: 8950

South Asian (SAS) AF: 0.0000176 AC: 1 AN: 56690

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26380

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2674

European-Non Finnish (NFE) AF: 0.0000469 AC: 7 AN: 149100

Other (OTH) AF: 0.00 AC: 0 AN: 13456

GnomAD4 genome AF: 0.0000593 AC: 9 AN: 151862 Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 5 AN XY: 74224

African (AFR) AF: 0.0000724 AC: 3 AN: 41416

American (AMR) AF: 0.00 AC: 0 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5154

South Asian (SAS) AF: 0.00 AC: 0 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000737 AC: 5 AN: 67886

Other (OTH) AF: 0.000475 AC: 1 AN: 2104

Alfa AF: 0.00 Hom.: 409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.065
DANN	Benign	0.71
PhyloP100		-2.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3745526; hg19: chr19-51302202;