rs10502088

Positions:

• chr11-107410247-T-C

Variant summary

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

The NM_152434.3(CWF19L2):​c.1617+5962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,144 control chromosomes in the GnomAD database, including 316 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 0.041 (316 hom., cov: 32)
• Consequence: CWF19L2 NM_152434.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

CWF19L2 (HGNC:26508): (CWF19 like cell cycle control factor 2) Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CWF19L2	NM_152434.3	c.1617+5962A>G		intron_variant		ENST00000282251.10
CWF19L2	XM_047426419.1	c.189+5962A>G		intron_variant
CWF19L2	XR_007062452.1	n.1626+5962A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CWF19L2	ENST00000282251.10	c.1617+5962A>G		intron_variant		1	NM_152434.3	P1
CWF19L2	ENST00000431778.5	c.1260+5962A>G		intron_variant, NMD_transcript_variant		1
CWF19L2	ENST00000532251.1	c.1260+5962A>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6178 AN: 152024 Hom.: 317 Cov.: 32

Gnomad AFR AF: 0.00874

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0416

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0406 AC: 6174 AN: 152144 Hom.: 316 Cov.: 32 AF XY: 0.0477 AC XY: 3549 AN XY: 74344

Gnomad4 AFR AF: 0.00871

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0244

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0270 Hom.: 14

Bravo AF: 0.0400

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs10502088; hg19: chr11-107280973;