chr1-50171882-C-T

Position:

• chr1-50171882-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.251-5207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,996 control chromosomes in the GnomAD database, including 11,111 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 0.37 (11111 hom., cov: 32)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

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=-0.87).
• 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.251-5207C>T		intron_variant		ENST00000371824.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAVL4	ENST00000371824.7	c.251-5207C>T		intron_variant		1	NM_001144774.3	P4

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56581 AN: 151876 Hom.: 11100 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.373 AC: 56643 AN: 151996 Hom.: 11111 Cov.: 32 AF XY: 0.381 AC XY: 28273 AN XY: 74282

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.352

Alfa AF: 0.292 Hom.: 2014

Bravo AF: 0.373

Asia WGS AF: 0.588 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.48

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: rs1018670; hg19: chr1-50637554;