rs11256915

Variant names:

• chr10-10922525-G-A
• rs11256915
• ENST00000664101.1:n.1317C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-10922525-G-A
• chr10-10922525-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664101.1(LINC00710):​n.1317C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,014 control chromosomes in the GnomAD database, including 16,976 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 0.46 (16976 hom., cov: 33)
• Consequence: LINC00710 ENST00000664101.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 3 publications found

Genes affected

LINC00710 (HGNC:27386): (long intergenic non-protein coding RNA 710)

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]

CELF2 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy 97

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• undetermined early-onset epileptic encephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF2	NM_001326325.2	c.146+2526G>A		intron_variant	Intron 3 of 15		NP_001313254.1
CELF2	NM_001326327.2	c.89+2526G>A		intron_variant	Intron 2 of 14		NP_001313256.1
CELF2	NM_001326326.2	c.89+2526G>A		intron_variant	Intron 2 of 14		NP_001313255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00710	ENST00000664101.1	n.1317C>T		non_coding_transcript_exon_variant	Exon 6 of 6
CELF2	ENST00000637215.1	c.89+2526G>A		intron_variant	Intron 2 of 14	5		ENSP00000490185.1
CELF2	ENST00000636488.1	c.89+2526G>A		intron_variant	Intron 2 of 13	5		ENSP00000489955.1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69856 AN: 151896 Hom.: 16979 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.460 AC: 69860 AN: 152014 Hom.: 16976 Cov.: 33 AF XY: 0.457 AC XY: 33970 AN XY: 74308

African (AFR) AF: 0.324 AC: 13433 AN: 41446

American (AMR) AF: 0.413 AC: 6305 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3468

East Asian (EAS) AF: 0.220 AC: 1134 AN: 5162

South Asian (SAS) AF: 0.566 AC: 2729 AN: 4818

European-Finnish (FIN) AF: 0.519 AC: 5477 AN: 10548

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.548 AC: 37250 AN: 67978

Other (OTH) AF: 0.467 AC: 986 AN: 2110

Alfa AF: 0.517 Hom.: 14278

Bravo AF: 0.439

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.58
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs11256915; hg19: chr10-10964488;