10-10846131-G-T

Variant names:

• chr10-10846131-G-T
• rs118184393
• NM_001326325.2:c.85G>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001326325.2(CELF2):​c.85G>T​(p.Asp29Tyr) 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. 4/4 in silico tools predict 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: CELF2 NM_001326325.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

CELF2 (HGNC:2550): (CUGBP Elav-like family member 2) Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF2	NM_001326325.2	c.85G>T	p.Asp29Tyr	missense_variant	Exon 2 of 16		NP_001313254.1
CELF2	XM_047424482.1	c.85G>T	p.Asp29Tyr	missense_variant	Exon 2 of 16		XP_047280438.1
CELF2	XM_047424483.1	c.85G>T	p.Asp29Tyr	missense_variant	Exon 2 of 16		XP_047280439.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF2	ENST00000638035	c.-81G>T		5_prime_UTR_variant	Exon 2 of 15	5		ENSP00000490401.1
CELF2	ENST00000637215.1	c.53+47314G>T		intron_variant	Intron 1 of 14	5		ENSP00000490185.1
CELF2	ENST00000636488.1	c.53+47314G>T		intron_variant	Intron 1 of 13	5		ENSP00000489955.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 26

GnomAD4 genome Cov.: 32

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.53
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs118184393; hg19: chr10-10888094;