1-50151618-G-C

Variant names:

• chr1-50151618-G-C
• rs10888681
• NM_001144774.3:c.250+6421G>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.250+6421G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,028 control chromosomes in the GnomAD database, including 14,840 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 0.42 (14840 hom., cov: 32)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• 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=-0.94).
• 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.250+6421G>C		intron	N/A	NP_001138246.1
	ELAVL4	NM_001438735.1		c.358+6421G>C		intron	N/A	NP_001425664.1
	ELAVL4	NM_001144775.3		c.358+6421G>C		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.250+6421G>C		intron	N/A	ENSP00000360889.2
	ELAVL4	ENST00000357083.8	TSL:1	c.358+6421G>C		intron	N/A	ENSP00000349594.5
	ELAVL4	ENST00000371823.8	TSL:1	c.250+6421G>C		intron	N/A	ENSP00000360888.4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64094 AN: 151910 Hom.: 14817 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.422 AC: 64177 AN: 152028 Hom.: 14840 Cov.: 32 AF XY: 0.427 AC XY: 31755 AN XY: 74312

African (AFR) AF: 0.581 AC: 24090 AN: 41448

American (AMR) AF: 0.377 AC: 5755 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3470

East Asian (EAS) AF: 0.774 AC: 3995 AN: 5160

South Asian (SAS) AF: 0.473 AC: 2277 AN: 4816

European-Finnish (FIN) AF: 0.362 AC: 3823 AN: 10570

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21816 AN: 67984

Other (OTH) AF: 0.387 AC: 817 AN: 2110

Alfa AF: 0.366 Hom.: 1419

Bravo AF: 0.431

Asia WGS AF: 0.592 AC: 2054 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.45
PhyloP100		-0.47
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: rs10888681; hg19: chr1-50617290;