19-50798945-T-A

Variant names:

• chr19-50798945-T-A
• rs3745526
• ENST00000595794.5:n.512A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000595794.5(C19orf48P):​n.512A>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 0.289 in 451,572 control chromosomes in the GnomAD database, including 21,197 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 (6189 hom., cov: 33)
  • Exomes 𝑓: 0.30 (15008 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• 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 rank	MANE	Protein	UniProt
C19orf48P	NR_171554.1	n.303A>T		non_coding_transcript_exon_variant	Exon 5 of 5
C19orf48P	NR_171555.1	n.142A>T		non_coding_transcript_exon_variant	Exon 4 of 4
C19orf48P	NR_171556.1	n.647A>T		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>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
C19orf48P	ENST00000598463.5	n.603A>T		non_coding_transcript_exon_variant	Exon 5 of 5	1
C19orf48P	ENST00000593287.5	n.478A>T		non_coding_transcript_exon_variant	Exon 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39974 AN: 151720 Hom.: 6181 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.302 AC: 90401 AN: 299734 Hom.: 15008 Cov.: 0 AF XY: 0.308 AC XY: 51744 AN XY: 168160

African (AFR) AF: 0.147 AC: 1223 AN: 8336

American (AMR) AF: 0.205 AC: 5136 AN: 25094

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 2131 AN: 9494

East Asian (EAS) AF: 0.644 AC: 5747 AN: 8922

South Asian (SAS) AF: 0.346 AC: 19586 AN: 56604

European-Finnish (FIN) AF: 0.384 AC: 10103 AN: 26334

Middle Eastern (MID) AF: 0.221 AC: 591 AN: 2674

European-Non Finnish (NFE) AF: 0.282 AC: 41930 AN: 148840

Other (OTH) AF: 0.294 AC: 3954 AN: 13436

GnomAD4 genome AF: 0.263 AC: 39996 AN: 151838 Hom.: 6189 Cov.: 33 AF XY: 0.270 AC XY: 20036 AN XY: 74216

African (AFR) AF: 0.154 AC: 6369 AN: 41408

American (AMR) AF: 0.224 AC: 3413 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 810 AN: 3466

East Asian (EAS) AF: 0.654 AC: 3369 AN: 5154

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4812

European-Finnish (FIN) AF: 0.385 AC: 4061 AN: 10554

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19297 AN: 67878

Other (OTH) AF: 0.264 AC: 554 AN: 2100

Alfa AF: 0.169 Hom.: 409

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	-0.79
CADD	Benign	0.053
DANN	Benign	0.57
PhyloP100		-2.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=299/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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; COSMIC: COSV54516574; COSMIC: COSV54516574;