chr1-50139665-T-C

Variant names:

• chr1-50139665-T-C
• rs3902720
• NM_001144774.3:c.10-5292T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144774.3(ELAVL4):​c.10-5292T>C 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 151,960 control chromosomes in the GnomAD database, including 11,288 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 0.38 (11288 hom., cov: 32)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.10-5292T>C		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.10-5292T>C		intron_variant	Intron 1 of 6	1	NM_001144774.3	ENSP00000360889.2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56930 AN: 151838 Hom.: 11276 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.375 AC: 56996 AN: 151960 Hom.: 11288 Cov.: 32 AF XY: 0.382 AC XY: 28407 AN XY: 74304

African (AFR) AF: 0.419 AC: 17382 AN: 41444

American (AMR) AF: 0.358 AC: 5458 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3470

East Asian (EAS) AF: 0.774 AC: 3994 AN: 5158

South Asian (SAS) AF: 0.472 AC: 2270 AN: 4810

European-Finnish (FIN) AF: 0.363 AC: 3838 AN: 10570

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21721 AN: 67942

Other (OTH) AF: 0.358 AC: 752 AN: 2102

Alfa AF: 0.333 Hom.: 27407

Bravo AF: 0.377

Asia WGS AF: 0.584 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3902720; hg19: chr1-50605337;