rs10905868

Positions:

• chr10-10932293-A-G

Variant summary

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

The ENST00000666257.1(LINC00710):​n.1673-2638T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,994 control chromosomes in the GnomAD database, including 4,404 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 0.24 (4404 hom., cov: 31)
• Consequence: LINC00710 ENST00000666257.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326317.2	c.-20+12294A>G		intron_variant			NP_001313246.1
CELF2	NM_001326318.2	c.-20+12294A>G		intron_variant			NP_001313247.1
CELF2	NM_001326319.2	c.-57-8124A>G		intron_variant			NP_001313248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00710	ENST00000666257.1	n.1673-2638T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35901 AN: 151876 Hom.: 4396 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.236 AC: 35933 AN: 151994 Hom.: 4404 Cov.: 31 AF XY: 0.236 AC XY: 17530 AN XY: 74302

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.210

Alfa AF: 0.222 Hom.: 3912

Bravo AF: 0.231

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10905868; hg19: chr10-10974256;