rs4802741

chr19-50798199-G-Achr19-50798199-G-C

Variant summary

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

The NR_171557.1(C19orf48P):n.824C>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 0.291 in 1,610,044 control chromosomes in the GnomAD database, including 73,222 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 (6183 hom., cov: 33)
  • Exomes 𝑓: 0.29 (67039 hom.)
• Consequence: C19orf48P NR_171557.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

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=7.06823E-6).
• 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	UniProt
C19orf48P	NR_171557.1	n.824C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C19orf48P	ENST00000641539.1	n.712C>T		non_coding_transcript_exon_variant	1/1
C19orf48P	ENST00000641834.2	n.1223C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39909 AN: 151998 Hom.: 6176 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

GnomAD3 exomes AF: 0.304 AC: 75583 AN: 248280 Hom.: 13356 AF XY: 0.308 AC XY: 41325 AN XY: 134054

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.205

Gnomad ASJ exome AF: 0.224

Gnomad EAS exome AF: 0.651

Gnomad SAS exome AF: 0.347

Gnomad FIN exome AF: 0.387

Gnomad NFE exome AF: 0.282

Gnomad OTH exome AF: 0.282

GnomAD4 exome AF: 0.294 AC: 428034 AN: 1457928 Hom.: 67039 Cov.: 35 AF XY: 0.295 AC XY: 213938 AN XY: 724860

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.207

Gnomad4 ASJ exome AF: 0.223

Gnomad4 EAS exome AF: 0.645

Gnomad4 SAS exome AF: 0.349

Gnomad4 FIN exome AF: 0.385

Gnomad4 NFE exome AF: 0.282

Gnomad4 OTH exome AF: 0.292

GnomAD4 genome AF: 0.262 AC: 39930 AN: 152116 Hom.: 6183 Cov.: 33 AF XY: 0.269 AC XY: 19993 AN XY: 74336

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: 0.264

Alfa AF: 0.272 Hom.: 9671

Bravo AF: 0.244

TwinsUK AF: 0.294 AC: 1092

ALSPAC AF: 0.291 AC: 1120

ESP6500AA AF: 0.155 AC: 682

ESP6500EA AF: 0.281 AC: 2414

ExAC AF: 0.306 AC: 37156

Asia WGS AF: 0.487 AC: 1689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.062
BayesDel_addAF	Benign	-0.83	T
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.3
Dann	Benign	0.51
DEOGEN2	Benign	0.00037	T;T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.059	N
LIST_S2	Benign	0.43	T;.
MetaRNN	Benign	0.0000071	T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.34	N;N
MutationTaster	Benign	1.0	P;P
PROVEAN	Benign	-0.62	N;N
REVEL	Benign	0.014
Sift4G	Benign	0.17	T;T
Polyphen		0.0020	B;B
Vest4		0.017
ClinPred		0.000024	T
GERP RS		0.84
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0
Varity_R		0.16
gMVP		0.022

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: rs4802741; hg19: chr19-51301456; COSMIC: COSV54516431; COSMIC: COSV54516431;