rs3745526

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-50798945-T-A
• chr19-50798945-T-C
• chr19-50798945-T-G

Variant summary

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

The NR_171559.1(C19orf48P):​n.131A>T variant causes a splice region, 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. 1/1 splice prediction tools predict no significant impact on normal splicing. 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 NR_171559.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

C19orf48P (HGNC:29667): (chromosome 19 open reading frame 48, pseudogene)

SNORD88B (HGNC:32748): (small nucleolar RNA, C/D box 88B)

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR exome AF: 0.147

Gnomad4 AMR exome AF: 0.205

Gnomad4 ASJ exome AF: 0.224

Gnomad4 EAS exome AF: 0.644

Gnomad4 SAS exome AF: 0.346

Gnomad4 FIN exome AF: 0.384

Gnomad4 NFE exome AF: 0.282

Gnomad4 OTH exome AF: 0.294

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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.264

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs3745526; hg19: chr19-51302202; COSMIC: COSV54516574; COSMIC: COSV54516574;