1-50148004-T-G

Position:

• chr1-50148004-T-G

Variant summary

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

The NM_001144774.3(ELAVL4):​c.250+2807T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,078 control chromosomes in the GnomAD database, including 6,610 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 0.29 (6610 hom., cov: 32)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

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 (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELAVL4	NM_001144774.3	c.250+2807T>G		intron_variant		ENST00000371824.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAVL4	ENST00000371824.7	c.250+2807T>G		intron_variant		1	NM_001144774.3	P4

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44340 AN: 151960 Hom.: 6608 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.292 AC: 44365 AN: 152078 Hom.: 6610 Cov.: 32 AF XY: 0.291 AC XY: 21659 AN XY: 74348

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.287

Alfa AF: 0.252 Hom.: 4876

Bravo AF: 0.301

Asia WGS AF: 0.329 AC: 1141 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	0.0090
DANN	Benign	0.57

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: rs4412638; hg19: chr1-50613676;