rs783562

Variant names:

• chr9-23823401-G-A
• rs783562
• NM_004432.5:c.-16+2405C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-23823401-G-A
• chr9-23823401-G-C
• chr9-23823401-G-T

Variant summary

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

The NM_004432.5(ELAVL2):​c.-16+2405C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,964 control chromosomes in the GnomAD database, including 13,177 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 0.41 (13177 hom., cov: 32)
• Consequence: ELAVL2 NM_004432.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 3 publications found

Genes affected

ELAVL2 (HGNC:3313): (ELAV like RNA binding protein 2) In humans, the ELAV like RNA binding protein gene family has four members (ELAVL1-4). ELAVL RNA binding proteins recognize AU-rich elements in the 3' UTRs of gene transcripts and thereby regulate gene expression post-transcriptionally. The protein encoded by this gene binds to several 3' UTRs, including its own and also that of FOS, ID, and POU5F1. This gene encodes ELAVL2 and, like ELAVL3 and ELAVL4, is expressed specifically in neurons and primarily localizes to the cytoplasm. This protein also forms a cytosolic complex with the normally nuclear-localized ELAVL1 protein. Alternative splicing of this gene results in multiple transcript variants encoding distinct protein isoforms. [provided by RefSeq, Jul 2020]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAVL2	NM_004432.5	c.-16+2405C>T		intron_variant	Intron 1 of 6	ENST00000397312.7	NP_004423.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAVL2	ENST00000397312.7	c.-16+2405C>T		intron_variant	Intron 1 of 6	1	NM_004432.5	ENSP00000380479.2
ELAVL2	ENST00000380117.5	c.-13+2405C>T		intron_variant	Intron 1 of 6	1		ENSP00000369460.1
ELAVL2	ENST00000462649.1	n.369+2405C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61955 AN: 151846 Hom.: 13122 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.408 AC: 62068 AN: 151964 Hom.: 13177 Cov.: 32 AF XY: 0.419 AC XY: 31093 AN XY: 74270

African (AFR) AF: 0.380 AC: 15738 AN: 41434

American (AMR) AF: 0.524 AC: 8001 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3462

East Asian (EAS) AF: 0.662 AC: 3412 AN: 5152

South Asian (SAS) AF: 0.440 AC: 2118 AN: 4818

European-Finnish (FIN) AF: 0.488 AC: 5147 AN: 10548

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25271 AN: 67956

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.383 Hom.: 5744

Bravo AF: 0.412

Asia WGS AF: 0.552 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.9
DANN	Benign	0.81
PhyloP100		-0.092
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: rs783562; hg19: chr9-23823399; COSMIC: COSV56369731; COSMIC: COSV56369731;