rs11583200

chr1-50094148-C-T

Variant summary

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

The NM_001324208.2(ELAVL4):c.18+45966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,040 control chromosomes in the GnomAD database, including 19,589 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 0.48 (19589 hom., cov: 33)
• Consequence: ELAVL4 NM_001324208.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELAVL4	NM_001144777.3	c.18+45966C>T		intron_variant
ELAVL4	NM_001324208.2	c.18+45966C>T		intron_variant
ELAVL4	XM_017000542.1	c.18+45966C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAVL4	ENST00000448907.7	c.18+45966C>T		intron_variant		2
ELAVL4	ENST00000463650.2	c.-13+46424C>T		intron_variant		5
ELAVL4	ENST00000651693.1	c.-125-3762C>T		intron_variant, NMD_transcript_variant
ELAVL4	ENST00000652252.1	n.237+26664C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73048 AN: 151922 Hom.: 19590 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.481 AC: 73058 AN: 152040 Hom.: 19589 Cov.: 33 AF XY: 0.473 AC XY: 35184 AN XY: 74314

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.516

Alfa AF: 0.589 Hom.: 52922

Bravo AF: 0.470

Asia WGS AF: 0.281 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
Dann	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11583200; hg19: chr1-50559820;