rs10491817

Variant names:

• chr9-23769756-A-C
• rs10491817
• NM_004432.5:c.-15-7507T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-23769756-A-C
• chr9-23769756-A-G

Variant summary

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

The NM_001351455.2(ELAVL2):​c.-19-4657T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0881 in 152,258 control chromosomes in the GnomAD database, including 675 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 0.088 (675 hom., cov: 32)
• Consequence: ELAVL2 NM_001351455.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351455.2. 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
	ELAVL2	NM_004432.5	MANE Select	c.-15-7507T>G		intron	N/A	NP_004423.2
	ELAVL2	NM_001351455.2		c.-19-4657T>G		intron	N/A	NP_001338384.1
	ELAVL2	NM_001385697.1		c.-19-4657T>G		intron	N/A	NP_001372626.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAVL2	ENST00000397312.7	TSL:1 MANE Select	c.-15-7507T>G		intron	N/A	ENSP00000380479.2
	ELAVL2	ENST00000380117.5	TSL:1	c.-12-7510T>G		intron	N/A	ENSP00000369460.1
	ELAVL2	ENST00000223951.10	TSL:1	c.-15-7507T>G		intron	N/A	ENSP00000223951.5

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 13401 AN: 152140 Hom.: 675 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0881 AC: 13418 AN: 152258 Hom.: 675 Cov.: 32 AF XY: 0.0908 AC XY: 6758 AN XY: 74442

African (AFR) AF: 0.0891 AC: 3705 AN: 41566

American (AMR) AF: 0.114 AC: 1748 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 571 AN: 3472

East Asian (EAS) AF: 0.105 AC: 544 AN: 5166

South Asian (SAS) AF: 0.0966 AC: 466 AN: 4824

European-Finnish (FIN) AF: 0.0896 AC: 950 AN: 10604

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0752 AC: 5117 AN: 68016

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.0475 Hom.: 47

Bravo AF: 0.0929

Asia WGS AF: 0.0930 AC: 324 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	0.71
PhyloP100		0.77
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: rs10491817; hg19: chr9-23769754;