1-50130785-A-G

Variant names:

• chr1-50130785-A-G
• rs5000809
• NM_001144774.3:c.10-14172A>G

Variant summary

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

The NM_001144774.3(ELAVL4):​c.10-14172A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,916 control chromosomes in the GnomAD database, including 11,269 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 (11269 hom., cov: 32)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

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=-0.88).
• 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 rank	MANE	Protein	UniProt
ELAVL4	NM_001144774.3	c.10-14172A>G		intron_variant	Intron 1 of 6	ENST00000371824.7	NP_001138246.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAVL4	ENST00000371824.7	c.10-14172A>G		intron_variant	Intron 1 of 6	1	NM_001144774.3	ENSP00000360889.2

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56833 AN: 151798 Hom.: 11258 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.375 AC: 56896 AN: 151916 Hom.: 11269 Cov.: 32 AF XY: 0.382 AC XY: 28339 AN XY: 74234

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.356

Alfa AF: 0.352 Hom.: 1176

Bravo AF: 0.376

Asia WGS AF: 0.585 AC: 2028 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.3
DANN	Benign	0.70

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: rs5000809; hg19: chr1-50596457;