NM_001144774.3:c.251-5207C>T

Variant names:

• chr1-50171882-C-T
• rs1018670
• NM_001144774.3:c.251-5207C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144774.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAVL4	NM_001144774.3	MANE Select	c.251-5207C>T		intron	N/A	NP_001138246.1
	ELAVL4	NM_001438735.1		c.359-5207C>T		intron	N/A	NP_001425664.1
	ELAVL4	NM_001144775.3		c.359-5207C>T		intron	N/A	NP_001138247.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAVL4	ENST00000371824.7	TSL:1 MANE Select	c.251-5207C>T		intron	N/A	ENSP00000360889.2
	ELAVL4	ENST00000357083.8	TSL:1	c.359-5207C>T		intron	N/A	ENSP00000349594.5
	ELAVL4	ENST00000371823.8	TSL:1	c.251-5207C>T		intron	N/A	ENSP00000360888.4

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

African (AFR) AF: 0.402 AC: 16664 AN: 41426

American (AMR) AF: 0.355 AC: 5424 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3470

East Asian (EAS) AF: 0.774 AC: 4004 AN: 5174

South Asian (SAS) AF: 0.495 AC: 2384 AN: 4814

European-Finnish (FIN) AF: 0.369 AC: 3901 AN: 10568

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

European-Non Finnish (NFE) AF: 0.322 AC: 21890 AN: 67964

Other (OTH) AF: 0.352 AC: 742 AN: 2106

Alfa AF: 0.303 Hom.: 2688

Bravo AF: 0.373

Asia WGS AF: 0.588 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		-0.19
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: rs1018670; hg19: chr1-50637554;