chr19-50798897-G-A

Variant names:

• chr19-50798897-G-A
• rs1043315
• ENST00000595794.5:n.560C>T

Variant summary

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

The ENST00000595794.5(C19orf48P):​n.560C>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 0.293 in 402,388 control chromosomes in the GnomAD database, including 19,420 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 0.27 (6408 hom., cov: 33)
  • Exomes 𝑓: 0.31 (13012 hom.)
• Consequence: C19orf48P ENST00000595794.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 13 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595794.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	NR_171554.1		n.351C>T		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	NR_171555.1		n.190C>T		non_coding_transcript_exon	Exon 4 of 4
	C19orf48P	NR_171556.1		n.695C>T		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	ENST00000595794.5	TSL:1	n.560C>T		non_coding_transcript_exon	Exon 3 of 3
	C19orf48P	ENST00000598463.5	TSL:1	n.651C>T		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	ENST00000593287.5	TSL:5	n.526C>T		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41231 AN: 151938 Hom.: 6400 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.307 AC: 76833 AN: 250332 Hom.: 13012 Cov.: 0 AF XY: 0.313 AC XY: 42552 AN XY: 136052

African (AFR) AF: 0.168 AC: 1147 AN: 6832

American (AMR) AF: 0.208 AC: 3684 AN: 17702

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 1400 AN: 6348

East Asian (EAS) AF: 0.644 AC: 5394 AN: 8370

South Asian (SAS) AF: 0.348 AC: 16625 AN: 47822

European-Finnish (FIN) AF: 0.383 AC: 9532 AN: 24888

Middle Eastern (MID) AF: 0.230 AC: 550 AN: 2396

European-Non Finnish (NFE) AF: 0.282 AC: 35068 AN: 124490

Other (OTH) AF: 0.299 AC: 3433 AN: 11484

GnomAD4 genome AF: 0.271 AC: 41255 AN: 152056 Hom.: 6408 Cov.: 33 AF XY: 0.277 AC XY: 20604 AN XY: 74308

African (AFR) AF: 0.182 AC: 7553 AN: 41484

American (AMR) AF: 0.228 AC: 3479 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3360 AN: 5150

South Asian (SAS) AF: 0.379 AC: 1826 AN: 4814

European-Finnish (FIN) AF: 0.383 AC: 4052 AN: 10586

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

European-Non Finnish (NFE) AF: 0.284 AC: 19315 AN: 67956

Other (OTH) AF: 0.270 AC: 569 AN: 2106

Alfa AF: 0.258 Hom.: 2035

Bravo AF: 0.254

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.90
DANN	Benign	0.55
PhyloP100		-1.7
Mutation Taster		=131/169	disease causing

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

Other links and lift over

dbSNP: rs1043315; hg19: chr19-51302154; COSMIC: COSV54516572; COSMIC: COSV54516572;