19-13759339-C-G

Variant names:

• chr19-13759339-C-G
• rs371671
• NM_030818.4:c.573+67C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030818.4(YJU2B):​c.573+67C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: YJU2B NM_030818.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.50
• Publications: 38 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030818.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YJU2B	NM_030818.4	MANE Select	c.573+67C>G		intron	N/A	NP_110445.1
	YJU2B	NM_001320561.2		c.573+67C>G		intron	N/A	NP_001307490.1
	YJU2B	NM_001320564.2		c.573+67C>G		intron	N/A	NP_001307493.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YJU2B	ENST00000221554.13	TSL:1 MANE Select	c.573+67C>G		intron	N/A	ENSP00000221554.7
	YJU2B	ENST00000588809.1	TSL:3	c.554C>G	p.Pro185Arg	missense	Exon 5 of 5	ENSP00000465392.1
	YJU2B	ENST00000589096.1	TSL:6	c.*249C>G		3_prime_UTR	Exon 1 of 1	ENSP00000467202.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 16

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0020
DANN	Benign	0.19
PhyloP100		-6.5
PromoterAI		-0.069	Neutral

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: rs371671; hg19: chr19-13870153;