chr11-107410247-T-C

Variant names:

• chr11-107410247-T-C
• rs10502088
• NM_152434.3:c.1617+5962A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CWF19L2	NM_152434.3	c.1617+5962A>G		intron_variant	Intron 10 of 17	ENST00000282251.10	NP_689647.2
CWF19L2	XM_047426419.1	c.189+5962A>G		intron_variant	Intron 3 of 10		XP_047282375.1
CWF19L2	XR_007062452.1	n.1626+5962A>G		intron_variant	Intron 10 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CWF19L2	ENST00000282251.10	c.1617+5962A>G		intron_variant	Intron 10 of 17	1	NM_152434.3	ENSP00000282251.5
CWF19L2	ENST00000431778.5	n.1260+5962A>G		intron_variant	Intron 7 of 15	1		ENSP00000411736.1
CWF19L2	ENST00000532251.1	n.1260+5962A>G		intron_variant	Intron 7 of 14	1		ENSP00000434704.1

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

African (AFR) AF: 0.00871 AC: 362 AN: 41544

American (AMR) AF: 0.105 AC: 1600 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1122 AN: 5144

South Asian (SAS) AF: 0.0452 AC: 218 AN: 4822

European-Finnish (FIN) AF: 0.0939 AC: 992 AN: 10568

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0244 AC: 1662 AN: 68010

Other (OTH) AF: 0.0407 AC: 86 AN: 2114

Alfa AF: 0.0413 Hom.: 99

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
PhyloP100		-0.048
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10502088; hg19: chr11-107280973;