15-72318508-C-T

Variant names:

• chr15-72318508-C-T
• rs2009365
• NM_052840.5:c.262+1105G>A

Variant summary

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

The NM_052840.5(CELF6):​c.262+1105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,038 control chromosomes in the GnomAD database, including 57,095 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 0.84 (57095 hom., cov: 31)
• Consequence: CELF6 NM_052840.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 2 publications found

Genes affected

CELF6 (HGNC:14059): (CUGBP Elav-like family member 6) 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]

ENSG00000260729 (HGNC:):

CELF6-AS1 (HGNC:58304):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052840.5. 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
	CELF6	NM_052840.5	MANE Select	c.262+1105G>A		intron	N/A	NP_443072.3
	CELF6	NM_001172684.2		c.262+1105G>A		intron	N/A	NP_001166155.1	Q96J87-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF6	ENST00000287202.10	TSL:1 MANE Select	c.262+1105G>A		intron	N/A	ENSP00000287202.5	Q96J87-1
	ENSG00000260729	ENST00000379915.4	TSL:2	n.*1014+1105G>A		intron	N/A	ENSP00000478716.1	A0A087WUJ7
	ENSG00000273025	ENST00000569547.1	TSL:2	n.262+1105G>A		intron	N/A	ENSP00000454749.1

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127297 AN: 151920 Hom.: 57101 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.837 AC: 127322 AN: 152038 Hom.: 57095 Cov.: 31 AF XY: 0.841 AC XY: 62536 AN XY: 74348

African (AFR) AF: 0.482 AC: 19930 AN: 41378

American (AMR) AF: 0.892 AC: 13612 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3470 AN: 3472

East Asian (EAS) AF: 0.943 AC: 4879 AN: 5172

South Asian (SAS) AF: 0.994 AC: 4803 AN: 4832

European-Finnish (FIN) AF: 0.962 AC: 10192 AN: 10596

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.991 AC: 67404 AN: 68008

Other (OTH) AF: 0.871 AC: 1835 AN: 2106

Alfa AF: 0.938 Hom.: 77914

Bravo AF: 0.814

Asia WGS AF: 0.931 AC: 3237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.5
DANN	Benign	0.67
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2009365; hg19: chr15-72610849;