rs1044833

Variant names:

• chr12-30710471-C-A
• rs1044833
• ENST00000417045.5:c.2856G>T

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The ENST00000417045.5(CAPRIN2):​c.2856G>T​(p.Gln952His) variant causes a missense 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: CAPRIN2 ENST00000417045.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.23
• Publications: 0 publications found

Genes affected

CAPRIN2 (HGNC:21259): (caprin family member 2) The protein encoded by this gene may regulate the transport of mRNA. It may play a role in the differentiation of erythroblasts. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417045.5. 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
	CAPRIN2	NM_001385503.1	MANE Select	c.2570-1G>T		splice_acceptor intron	N/A	NP_001372432.1
	CAPRIN2	NM_001385516.1		c.2859G>T	p.Gln953His	missense	Exon 18 of 18	NP_001372445.1
	CAPRIN2	NM_032156.5		c.2856G>T	p.Gln952His	missense	Exon 18 of 18	NP_115532.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPRIN2	ENST00000417045.5	TSL:1	c.2856G>T	p.Gln952His	missense	Exon 18 of 18	ENSP00000391479.1
	CAPRIN2	ENST00000395805.6	TSL:1	c.2691G>T	p.Gln897His	missense	Exon 17 of 17	ENSP00000379150.2
	CAPRIN2	ENST00000695402.1	MANE Select	c.2570-1G>T		splice_acceptor intron	N/A	ENSP00000511883.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Benign	-0.60
CADD	Benign	23
DANN	Uncertain	0.99
Eigen	Benign	0.051
Eigen_PC	Benign	0.21
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Benign	0.0050	T
PhyloP100		3.2
ClinPred		0.91	D
GERP RS		4.9
Mutation Taster		=4/96	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.62		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.62		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1044833; hg19: chr12-30863405;