rs967582

chr1-50116500-A-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ELAVL4	NM_001144774.3	c.9+7302A>C		intron_variant		ENST00000371824.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAVL4	ENST00000371824.7	c.9+7302A>C		intron_variant		1	NM_001144774.3	P4

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

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.396

Alfa AF: 0.361 Hom.: 13659

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

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: rs967582; hg19: chr1-50582172;