NM_007185.7:c.1026G>A

Variant names:

• chr1-151706324-C-T
• rs140590829
• NM_007185.7:c.1026G>A

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Moderate BP6_Moderate BP7

The NM_007185.7(CELF3):​c.1026G>A​(p.Ala342Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000322 in 1,553,274 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00021 (1 hom.)
• Consequence: CELF3 NM_007185.7 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.60
• Publications: 0 publications found

Genes affected

CELF3 (HGNC:11967): (CUGBP Elav-like family member 3) 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. Multiple alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Feb 2010]

ENSG00000227045 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.082).
• BP6: Variant 1-151706324-C-T is Benign according to our data. Variant chr1-151706324-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2639180.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.6 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007185.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF3	NM_007185.7	MANE Select	c.1026G>A	p.Ala342Ala	synonymous	Exon 10 of 13	NP_009116.3
	CELF3	NM_001291106.2		c.1023G>A	p.Ala341Ala	synonymous	Exon 10 of 13	NP_001278035.1	Q5SZQ8-2
	CELF3	NM_001291107.2		c.1023G>A	p.Ala341Ala	synonymous	Exon 10 of 13	NP_001278036.1	Q5SZQ8-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF3	ENST00000290583.9	TSL:1 MANE Select	c.1026G>A	p.Ala342Ala	synonymous	Exon 10 of 13	ENSP00000290583.4	Q5SZQ8-1
	CELF3	ENST00000290585.8	TSL:1	c.876G>A	p.Ala292Ala	synonymous	Exon 9 of 12	ENSP00000290585.4	Q5SZQ8-4
	CELF3	ENST00000420342.1	TSL:5	c.1026G>A	p.Ala342Ala	synonymous	Exon 11 of 14	ENSP00000402503.1	H0Y623

Frequencies

GnomAD3 genomes AF: 0.00137 AC: 208 AN: 152174 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00475

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000332 AC: 52 AN: 156492 AF XY: 0.000255

Gnomad AFR exome AF: 0.00511

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000839

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000208 AC: 292 AN: 1400982 Hom.: 1 Cov.: 32 AF XY: 0.000182 AC XY: 126 AN XY: 691308

African (AFR) AF: 0.00559 AC: 177 AN: 31642

American (AMR) AF: 0.0000279 AC: 1 AN: 35858

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25202

East Asian (EAS) AF: 0.0000279 AC: 1 AN: 35832

South Asian (SAS) AF: 0.0000252 AC: 2 AN: 79498

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49428

Middle Eastern (MID) AF: 0.000199 AC: 1 AN: 5026

European-Non Finnish (NFE) AF: 0.0000889 AC: 96 AN: 1080420

Other (OTH) AF: 0.000241 AC: 14 AN: 58076

GnomAD4 genome AF: 0.00137 AC: 208 AN: 152292 Hom.: 0 Cov.: 33 AF XY: 0.00132 AC XY: 98 AN XY: 74478

African (AFR) AF: 0.00474 AC: 197 AN: 41556

American (AMR) AF: 0.000131 AC: 2 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 68020

Other (OTH) AF: 0.00 AC: 0 AN: 2116

Alfa AF: 0.000753 Hom.: 0

Bravo AF: 0.00174

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	8.9
DANN	Benign	0.80
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs140590829; hg19: chr1-151678800;