chr1-50184027-C-T

Variant names:

• chr1-50184027-C-T
• rs3009113
• NM_001144774.3:c.354+6835C>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.354+6835C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,996 control chromosomes in the GnomAD database, including 19,213 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 0.47 (19213 hom., cov: 31)
• Consequence: ELAVL4 NM_001144774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAVL4	NM_001144774.3	MANE Select	c.354+6835C>T		intron	N/A	NP_001138246.1	P26378-2
	ELAVL4	NM_001438735.1		c.462+6835C>T		intron	N/A	NP_001425664.1
	ELAVL4	NM_001144775.3		c.462+6835C>T		intron	N/A	NP_001138247.2	A0A0R4J2E6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAVL4	ENST00000371824.7	TSL:1 MANE Select	c.354+6835C>T		intron	N/A	ENSP00000360889.2	P26378-2
	ELAVL4	ENST00000357083.8	TSL:1	c.462+6835C>T		intron	N/A	ENSP00000349594.5	A0A0R4J2E6
	ELAVL4	ENST00000371823.8	TSL:1	c.354+6835C>T		intron	N/A	ENSP00000360888.4	P26378-1

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70821 AN: 151878 Hom.: 19217 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.466 AC: 70817 AN: 151996 Hom.: 19213 Cov.: 31 AF XY: 0.457 AC XY: 33963 AN XY: 74294

African (AFR) AF: 0.210 AC: 8722 AN: 41464

American (AMR) AF: 0.546 AC: 8346 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2317 AN: 3468

East Asian (EAS) AF: 0.105 AC: 544 AN: 5172

South Asian (SAS) AF: 0.456 AC: 2191 AN: 4808

European-Finnish (FIN) AF: 0.478 AC: 5040 AN: 10538

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41855 AN: 67954

Other (OTH) AF: 0.545 AC: 1152 AN: 2112

Alfa AF: 0.542 Hom.: 37122

Bravo AF: 0.458

Asia WGS AF: 0.283 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.55
PhyloP100		-1.9
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: rs3009113; hg19: chr1-50649699; COSMIC: COSV63915471; COSMIC: COSV63915471;