rs371671

chr19-13759339-C-Achr19-13759339-C-G

Variant summary

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

The NM_030818.4(YJU2B):c.573+67C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 1,320,870 control chromosomes in the GnomAD database, including 145,095 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 0.53 (22593 hom., cov: 32)
  • Exomes 𝑓: 0.45 (122502 hom.)
• Consequence: YJU2B NM_030818.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.50

Genes affected

YJU2B (HGNC:28118): (YJU2 splicing factor homolog B) Involved in response to virus. Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YJU2B	NM_030818.4	c.573+67C>A		intron_variant		ENST00000221554.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YJU2B	ENST00000221554.13	c.573+67C>A		intron_variant		1	NM_030818.4	P1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80229 AN: 151840 Hom.: 22544 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.481

GnomAD3 exomes AF: 0.493 AC: 47391 AN: 96050 Hom.: 11994 AF XY: 0.491 AC XY: 24603 AN XY: 50088

Gnomad AFR exome AF: 0.759

Gnomad AMR exome AF: 0.436

Gnomad ASJ exome AF: 0.494

Gnomad EAS exome AF: 0.607

Gnomad SAS exome AF: 0.530

Gnomad FIN exome AF: 0.452

Gnomad NFE exome AF: 0.440

Gnomad OTH exome AF: 0.450

GnomAD4 exome AF: 0.452 AC: 528779 AN: 1168912 Hom.: 122502 Cov.: 16 AF XY: 0.453 AC XY: 261302 AN XY: 576412

Gnomad4 AFR exome AF: 0.748

Gnomad4 AMR exome AF: 0.425

Gnomad4 ASJ exome AF: 0.472

Gnomad4 EAS exome AF: 0.608

Gnomad4 SAS exome AF: 0.517

Gnomad4 FIN exome AF: 0.454

Gnomad4 NFE exome AF: 0.433

Gnomad4 OTH exome AF: 0.465

GnomAD4 genome AF: 0.529 AC: 80342 AN: 151958 Hom.: 22593 Cov.: 32 AF XY: 0.526 AC XY: 39097 AN XY: 74266

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.484

Alfa AF: 0.443 Hom.: 21579

Bravo AF: 0.536

Asia WGS AF: 0.597 AC: 2074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.0010
Dann	Benign	0.44

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: rs371671; hg19: chr19-13870153; COSMIC: COSV55584195; COSMIC: COSV55584195;