rs967582

Variant names:

• chr1-50116500-A-C
• rs967582
• NM_001144774.3:c.9+7302A>C

Variant summary

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

The NM_001144774.3(ELAVL4):​c.9+7302A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,584 control chromosomes in the GnomAD database, including 14,221 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 0.42 (14221 hom., cov: 31)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 11 publications found

Genes affected

ELAVL4 (HGNC:3315): (ELAV like RNA binding protein 4) Enables mRNA 3'-UTR AU-rich region binding activity; poly(A) binding activity; and pre-mRNA intronic pyrimidine-rich binding activity. Involved in 3'-UTR-mediated mRNA stabilization; RNA processing; and positive regulation of 3'-UTR-mediated mRNA stabilization. Predicted to be located in axon; cytoplasm; and dendrite. Predicted to be part of polysomal ribosome. Predicted to be active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAVL4	NM_001144774.3	c.9+7302A>C		intron_variant	Intron 1 of 6	ENST00000371824.7	NP_001138246.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAVL4	ENST00000371824.7	c.9+7302A>C		intron_variant	Intron 1 of 6	1	NM_001144774.3	ENSP00000360889.2

Frequencies

GnomAD3 genomes AF: 0.422 AC: 63931 AN: 151466 Hom.: 14200 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.422 AC: 63993 AN: 151584 Hom.: 14221 Cov.: 31 AF XY: 0.426 AC XY: 31504 AN XY: 74018

African (AFR) AF: 0.514 AC: 21246 AN: 41330

American (AMR) AF: 0.370 AC: 5624 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3470

East Asian (EAS) AF: 0.760 AC: 3894 AN: 5122

South Asian (SAS) AF: 0.377 AC: 1807 AN: 4792

European-Finnish (FIN) AF: 0.448 AC: 4693 AN: 10486

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24454 AN: 67872

Other (OTH) AF: 0.396 AC: 830 AN: 2098

Alfa AF: 0.371 Hom.: 20304

Bravo AF: 0.421

Asia WGS AF: 0.574 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		-0.38
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: rs967582; hg19: chr1-50582172;