1-50151618-G-C

Variant summary

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

The NM_001144774.3(ELAVL4):c.250+6421G>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 152,028 control chromosomes in the GnomAD database, including 14,840 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 (14840 hom., cov: 32)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELAVL4	NM_001144774.3	c.250+6421G>C		intron_variant		ENST00000371824.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAVL4	ENST00000371824.7	c.250+6421G>C		intron_variant		1	NM_001144774.3	P4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64094 AN: 151910 Hom.: 14817 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.422 AC: 64177 AN: 152028 Hom.: 14840 Cov.: 32 AF XY: 0.427 AC XY: 31755 AN XY: 74312

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.387

Alfa AF: 0.366 Hom.: 1419

Bravo AF: 0.431

Asia WGS AF: 0.592 AC: 2054 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.14
Dann	Benign	0.45

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: rs10888681; hg19: chr1-50617290;