rs372369954

Variant names:

• chr1-151706722-G-A
• rs372369954
• NM_007185.7:c.935C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-151706722-G-A
• chr1-151706722-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_007185.7(CELF3):​c.935C>T​(p.Ala312Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000361 in 1,550,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00014 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000025 (0 hom.)
• Consequence: CELF3 NM_007185.7 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.60
• 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 -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08870691).

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.935C>T	p.Ala312Val	missense	Exon 9 of 13	NP_009116.3
	CELF3	NM_001291106.2		c.935C>T	p.Ala312Val	missense	Exon 9 of 13	NP_001278035.1	Q5SZQ8-2
	CELF3	NM_001291107.2		c.932C>T	p.Ala311Val	missense	Exon 9 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.935C>T	p.Ala312Val	missense	Exon 9 of 13	ENSP00000290583.4	Q5SZQ8-1
	CELF3	ENST00000290585.8	TSL:1	c.785C>T	p.Ala262Val	missense	Exon 8 of 12	ENSP00000290585.4	Q5SZQ8-4
	CELF3	ENST00000420342.1	TSL:5	c.935C>T	p.Ala312Val	missense	Exon 10 of 14	ENSP00000402503.1	H0Y623

Frequencies

GnomAD3 genomes AF: 0.000138 AC: 21 AN: 152246 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

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: 0.0000588

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000532 AC: 8 AN: 150382 AF XY: 0.0000250

Gnomad AFR exome AF: 0.000527

Gnomad AMR exome AF: 0.0000816

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000250 AC: 35 AN: 1397798 Hom.: 0 Cov.: 32 AF XY: 0.0000160 AC XY: 11 AN XY: 689450

African (AFR) AF: 0.000570 AC: 18 AN: 31570

American (AMR) AF: 0.0000562 AC: 2 AN: 35578

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25056

East Asian (EAS) AF: 0.00 AC: 0 AN: 35728

South Asian (SAS) AF: 0.0000253 AC: 2 AN: 79126

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48934

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5574

European-Non Finnish (NFE) AF: 0.00000927 AC: 10 AN: 1078302

Other (OTH) AF: 0.0000518 AC: 3 AN: 57930

GnomAD4 genome AF: 0.000138 AC: 21 AN: 152246 Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13 AN XY: 74378

African (AFR) AF: 0.000362 AC: 15 AN: 41462

American (AMR) AF: 0.0000654 AC: 1 AN: 15294

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5194

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4836

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10632

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 68038

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.0000812 Hom.: 0

Bravo AF: 0.000219

ESP6500AA AF: 0.000266 AC: 1

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.0000206 AC: 1

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.48
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.13	T
Eigen	Benign	-0.11
Eigen_PC	Benign	-0.052
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.95	D
M_CAP	Benign	0.0053	T
MetaRNN	Benign	0.089	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.29	N
PhyloP100		4.6
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-0.64	N
REVEL	Benign	0.051
Sift	Benign	0.30	T
Sift4G	Benign	0.23	T
Polyphen		0.0080	B
Vest4		0.41
MVP		0.30
MPC		0.32
ClinPred		0.026	T
GERP RS		4.4
Varity_R		0.082
gMVP		0.42
Mutation Taster		=81/19	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs372369954; hg19: chr1-151679198;