rs9991

chr19-50797973-G-Achr19-50797973-G-Cchr19-50797973-G-T

Variant summary

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

The NR_171557.1(C19orf48P):n.1050C>T 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 0.28 in 998,930 control chromosomes in the GnomAD database, including 43,763 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 (6184 hom., cov: 33)
  • Exomes 𝑓: 0.28 (37579 hom.)
• Consequence: C19orf48P NR_171557.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

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=-0.82).
• 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.1050C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C19orf48P	ENST00000641834.2	n.1449C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39922 AN: 152032 Hom.: 6177 Cov.: 33

Gnomad AFR AF: 0.152

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: 0.255

GnomAD4 exome AF: 0.284 AC: 240104 AN: 846780 Hom.: 37579 Cov.: 11 AF XY: 0.286 AC XY: 121835 AN XY: 426256

Gnomad4 AFR exome AF: 0.136

Gnomad4 AMR exome AF: 0.206

Gnomad4 ASJ exome AF: 0.217

Gnomad4 EAS exome AF: 0.642

Gnomad4 SAS exome AF: 0.341

Gnomad4 FIN exome AF: 0.381

Gnomad4 NFE exome AF: 0.264

Gnomad4 OTH exome AF: 0.282

GnomAD4 genome AF: 0.263 AC: 39943 AN: 152150 Hom.: 6184 Cov.: 33 AF XY: 0.269 AC XY: 20005 AN XY: 74394

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.224

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: 0.263

Alfa AF: 0.269 Hom.: 7698

Bravo AF: 0.244

Asia WGS AF: 0.488 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.7
Dann	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs9991; hg19: chr19-51301230; COSMIC: COSV54517312; COSMIC: COSV54517312;