rs3009113

Positions:

• chr1-50184027-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144774.3(ELAVL4):​c.354+6835C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,996 control chromosomes in the GnomAD database, including 19,213 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 0.47 (19213 hom., cov: 31)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

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]

ELAVL4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELAVL4	NM_001144774.3	c.354+6835C>T		intron_variant		ENST00000371824.7	NP_001138246.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELAVL4	ENST00000371824.7	c.354+6835C>T		intron_variant		1	NM_001144774.3	ENSP00000360889.2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70821 AN: 151878 Hom.: 19217 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.466 AC: 70817 AN: 151996 Hom.: 19213 Cov.: 31 AF XY: 0.457 AC XY: 33963 AN XY: 74294

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.545

Alfa AF: 0.589 Hom.: 26857

Bravo AF: 0.458

Asia WGS AF: 0.283 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.55

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: rs3009113; hg19: chr1-50649699; COSMIC: COSV63915471; COSMIC: COSV63915471;