19-50798809-A-G

Position:

• chr19-50798809-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_171557.1(C19orf48P):​n.214T>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 0.293 in 460,806 control chromosomes in the GnomAD database, including 22,691 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 0.26 (6186 hom., cov: 33)
  • Exomes 𝑓: 0.31 (16505 hom.)
• Consequence: C19orf48P NR_171557.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C19orf48P	NR_171557.1	n.214T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C19orf48P	ENST00000641539.1	n.102T>C		non_coding_transcript_exon_variant	1/1
C19orf48P	ENST00000641834.2	n.613T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39955 AN: 151988 Hom.: 6178 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.308 AC: 95122 AN: 308700 Hom.: 16505 Cov.: 0 AF XY: 0.311 AC XY: 50794 AN XY: 163174

Gnomad4 AFR exome AF: 0.144

Gnomad4 AMR exome AF: 0.205

Gnomad4 ASJ exome AF: 0.221

Gnomad4 EAS exome AF: 0.645

Gnomad4 SAS exome AF: 0.346

Gnomad4 FIN exome AF: 0.381

Gnomad4 NFE exome AF: 0.277

Gnomad4 OTH exome AF: 0.293

GnomAD4 genome AF: 0.263 AC: 39977 AN: 152106 Hom.: 6186 Cov.: 33 AF XY: 0.269 AC XY: 20012 AN XY: 74346

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.264

Alfa AF: 0.268 Hom.: 9818

Bravo AF: 0.245

Asia WGS AF: 0.488 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3745528; hg19: chr19-51302066; COSMIC: COSV54518256; COSMIC: COSV54518256;