chr15-72318508-C-T

Position:

• chr15-72318508-C-T

Variant summary

Our verdict is Benign. Variant got -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

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:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF6	NM_052840.5	c.262+1105G>A		intron_variant		ENST00000287202.10	NP_443072.3
CELF6	NM_001172684.2	c.262+1105G>A		intron_variant			NP_001166155.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CELF6	ENST00000287202.10	c.262+1105G>A		intron_variant		1	NM_052840.5	ENSP00000287202.5
ENSG00000260729	ENST00000379915.4	n.*1014+1105G>A		intron_variant		2		ENSP00000478716.1
ENSG00000273025	ENST00000569547.1	n.262+1105G>A		intron_variant		2		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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.871

Alfa AF: 0.960 Hom.: 61006

Bravo AF: 0.814

Asia WGS AF: 0.931 AC: 3237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.5
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs2009365; hg19: chr15-72610849;