1-50089990-A-T

Variant names:

• chr1-50089990-A-T
• rs7520915
• NM_001324208.2:c.18+41808A>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+41808A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,888 control chromosomes in the GnomAD database, including 21,303 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 0.51 (21303 hom., cov: 30)
• Consequence: ELAVL4 NM_001324208.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 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+41808A>T		intron	N/A	NP_001311137.1
	ELAVL4	NM_001144777.3		c.18+41808A>T		intron	N/A	NP_001138249.1
	ELAVL4	NM_001438739.1		c.18+41808A>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+41808A>T		intron	N/A	ENSP00000399939.2
	ELAVL4	ENST00000463650.2	TSL:5	c.-13+42266A>T		intron	N/A	ENSP00000498680.1
	ELAVL4	ENST00000651693.1		n.-125-7920A>T		intron	N/A	ENSP00000498319.1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77532 AN: 151770 Hom.: 21302 Cov.: 30

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.511 AC: 77548 AN: 151888 Hom.: 21303 Cov.: 30 AF XY: 0.505 AC XY: 37446 AN XY: 74218

African (AFR) AF: 0.355 AC: 14709 AN: 41396

American (AMR) AF: 0.518 AC: 7902 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2469 AN: 3468

East Asian (EAS) AF: 0.118 AC: 608 AN: 5156

South Asian (SAS) AF: 0.469 AC: 2251 AN: 4798

European-Finnish (FIN) AF: 0.551 AC: 5804 AN: 10542

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42004 AN: 67940

Other (OTH) AF: 0.539 AC: 1139 AN: 2114

Alfa AF: 0.566 Hom.: 3145

Bravo AF: 0.502

Asia WGS AF: 0.306 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.0
DANN	Benign	0.72
PhyloP100		0.73
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: rs7520915; hg19: chr1-50555662;