19-50798138-C-T

Position:

• chr19-50798138-C-T

Variant summary

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

The NR_171557.1(C19orf48P):​n.885G>A 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 0.291 in 1,552,884 control chromosomes in the GnomAD database, including 70,653 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 (6168 hom., cov: 32)
  • Exomes 𝑓: 0.29 (64485 hom.)
• Consequence: C19orf48P NR_171557.1 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.2199035E-5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C19orf48P	NR_171557.1	n.885G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C19orf48P	ENST00000641834.2	n.1284G>A		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39875 AN: 151976 Hom.: 6161 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.254

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: 0.254

GnomAD3 exomes AF: 0.306 AC: 63016 AN: 205822 Hom.: 11352 AF XY: 0.309 AC XY: 33721 AN XY: 109106

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.203

Gnomad ASJ exome AF: 0.223

Gnomad EAS exome AF: 0.650

Gnomad SAS exome AF: 0.347

Gnomad FIN exome AF: 0.384

Gnomad NFE exome AF: 0.281

Gnomad OTH exome AF: 0.290

GnomAD4 exome AF: 0.294 AC: 411297 AN: 1400790 Hom.: 64485 Cov.: 34 AF XY: 0.295 AC XY: 203275 AN XY: 689568

Gnomad4 AFR exome AF: 0.141

Gnomad4 AMR exome AF: 0.205

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.645

Gnomad4 SAS exome AF: 0.349

Gnomad4 FIN exome AF: 0.384

Gnomad4 NFE exome AF: 0.282

Gnomad4 OTH exome AF: 0.292

GnomAD4 genome AF: 0.262 AC: 39896 AN: 152094 Hom.: 6168 Cov.: 32 AF XY: 0.269 AC XY: 19974 AN XY: 74354

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: 0.262

Alfa AF: 0.274 Hom.: 12089

Bravo AF: 0.244

TwinsUK AF: 0.294 AC: 1092

ALSPAC AF: 0.291 AC: 1120

ESP6500AA AF: 0.154 AC: 680

ESP6500EA AF: 0.281 AC: 2413

ExAC AF: 0.299 AC: 36036

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
AlphaMissense	Benign	0.095
BayesDel_addAF	Benign	-0.80	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.89
DANN	Benign	0.75
DEOGEN2	Benign	0.023	T;T
Eigen	Benign	-0.96
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.056	N
LIST_S2	Benign	0.29	T;.
MetaRNN	Benign	0.000012	T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.0	N;N
MutationTaster	Benign	1.0	P;P
PROVEAN	Pathogenic	-5.4	D;D
REVEL	Benign	0.098
Sift4G	Pathogenic	0.0	D;D
Polyphen		0.97	D;D
Vest4		0.079
ClinPred		0.052	T
GERP RS		-2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.32
gMVP		0.034

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; COSMIC: COSV54516254; COSMIC: COSV54516254;