chr1-50094148-C-T

Variant names:

• chr1-50094148-C-T
• rs11583200
• NM_001324208.2:c.18+45966C>T

Variant summary

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

The NM_001324208.2(ELAVL4):​c.18+45966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,040 control chromosomes in the GnomAD database, including 19,589 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 0.48 (19589 hom., cov: 33)
• Consequence: ELAVL4 NM_001324208.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 71 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001324208.2. 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_001324208.2		c.18+45966C>T		intron	N/A	NP_001311137.1
	ELAVL4	NM_001144777.3		c.18+45966C>T		intron	N/A	NP_001138249.1
	ELAVL4	NM_001438739.1		c.18+45966C>T		intron	N/A	NP_001425668.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAVL4	ENST00000448907.7	TSL:2	c.18+45966C>T		intron	N/A	ENSP00000399939.2
	ELAVL4	ENST00000463650.2	TSL:5	c.-13+46424C>T		intron	N/A	ENSP00000498680.1
	ELAVL4	ENST00000651693.1		n.-125-3762C>T		intron	N/A	ENSP00000498319.1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73048 AN: 151922 Hom.: 19590 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.481 AC: 73058 AN: 152040 Hom.: 19589 Cov.: 33 AF XY: 0.473 AC XY: 35184 AN XY: 74314

African (AFR) AF: 0.276 AC: 11447 AN: 41474

American (AMR) AF: 0.503 AC: 7680 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2389 AN: 3470

East Asian (EAS) AF: 0.101 AC: 520 AN: 5170

South Asian (SAS) AF: 0.463 AC: 2225 AN: 4806

European-Finnish (FIN) AF: 0.515 AC: 5438 AN: 10560

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.612 AC: 41626 AN: 67978

Other (OTH) AF: 0.516 AC: 1089 AN: 2110

Alfa AF: 0.571 Hom.: 106832

Bravo AF: 0.470

Asia WGS AF: 0.281 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.45
PhyloP100		-0.034
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11583200; hg19: chr1-50559820;