chr1-50155273-A-G

Variant names:

• chr1-50155273-A-G
• rs17105974
• NM_001144774.3:c.250+10076A>G

Variant summary

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

The NM_001144774.3(ELAVL4):​c.250+10076A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 147,222 control chromosomes in the GnomAD database, including 462 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 0.068 (462 hom., cov: 29)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAVL4	NM_001144774.3	c.250+10076A>G		intron_variant	Intron 2 of 6	ENST00000371824.7	NP_001138246.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAVL4	ENST00000371824.7	c.250+10076A>G		intron_variant	Intron 2 of 6	1	NM_001144774.3	ENSP00000360889.2

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10033 AN: 147116 Hom.: 459 Cov.: 29

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0355

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.000409

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.0788

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

GnomAD4 genome AF: 0.0682 AC: 10043 AN: 147222 Hom.: 462 Cov.: 29 AF XY: 0.0660 AC XY: 4713 AN XY: 71414

African (AFR) AF: 0.109 AC: 4328 AN: 39820

American (AMR) AF: 0.0586 AC: 837 AN: 14288

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3466

East Asian (EAS) AF: 0.000410 AC: 2 AN: 4878

South Asian (SAS) AF: 0.0243 AC: 113 AN: 4654

European-Finnish (FIN) AF: 0.0211 AC: 201 AN: 9548

Middle Eastern (MID) AF: 0.157 AC: 44 AN: 280

European-Non Finnish (NFE) AF: 0.0560 AC: 3769 AN: 67350

Other (OTH) AF: 0.0776 AC: 158 AN: 2036

Alfa AF: 0.0597 Hom.: 478

Bravo AF: 0.0724

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		0.49
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: rs17105974; hg19: chr1-50620945;