NM_001419.3:c.656+17C>T

Variant names:

• chr19-7967548-G-A
• rs3826740
• NM_001419.3:c.656+17C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001419.3(ELAVL1):​c.656+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,610,604 control chromosomes in the GnomAD database, including 52,295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3916 hom., cov: 33)
  • Exomes 𝑓: 0.25 (48379 hom.)
• Consequence: ELAVL1 NM_001419.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.495
• Publications: 7 publications found

Genes affected

ELAVL1 (HGNC:3312): (ELAV like RNA binding protein 1) The protein encoded by this gene is a member of the ELAVL family of RNA-binding proteins that contain several RNA recognition motifs, and selectively bind AU-rich elements (AREs) found in the 3' untranslated regions of mRNAs. AREs signal degradation of mRNAs as a means to regulate gene expression, thus by binding AREs, the ELAVL family of proteins play a role in stabilizing ARE-containing mRNAs. This gene has been implicated in a variety of biological processes and has been linked to a number of diseases, including cancer. It is highly expressed in many cancers, and could be potentially useful in cancer diagnosis, prognosis, and therapy. [provided by RefSeq, Sep 2012]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 19-7967548-G-A is Benign according to our data. Variant chr19-7967548-G-A is described in ClinVar as Benign. ClinVar VariationId is 1237796.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001419.3. 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
	ELAVL1	NM_001419.3	MANE Select	c.656+17C>T		intron	N/A	NP_001410.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELAVL1	ENST00000407627.7	TSL:1 MANE Select	c.656+17C>T		intron	N/A	ENSP00000385269.1	Q15717-1
	ELAVL1	ENST00000958865.1		c.932+17C>T		intron	N/A	ENSP00000628924.1
	ELAVL1	ENST00000596459.5	TSL:2	c.656+17C>T		intron	N/A	ENSP00000472197.1	Q15717-1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30587 AN: 152056 Hom.: 3915 Cov.: 33

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.204

GnomAD2 exomes AF: 0.262 AC: 64454 AN: 246424 AF XY: 0.261

Gnomad AFR exome AF: 0.0404

Gnomad AMR exome AF: 0.312

Gnomad ASJ exome AF: 0.242

Gnomad EAS exome AF: 0.495

Gnomad FIN exome AF: 0.275

Gnomad NFE exome AF: 0.247

Gnomad OTH exome AF: 0.252

GnomAD4 exome AF: 0.250 AC: 364888 AN: 1458430 Hom.: 48379 Cov.: 34 AF XY: 0.250 AC XY: 181215 AN XY: 725312

African (AFR) AF: 0.0376 AC: 1257 AN: 33422

American (AMR) AF: 0.305 AC: 13549 AN: 44388

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 6331 AN: 26082

East Asian (EAS) AF: 0.508 AC: 20139 AN: 39614

South Asian (SAS) AF: 0.232 AC: 19990 AN: 86084

European-Finnish (FIN) AF: 0.274 AC: 14597 AN: 53252

Middle Eastern (MID) AF: 0.222 AC: 1116 AN: 5016

European-Non Finnish (NFE) AF: 0.246 AC: 272729 AN: 1110388

Other (OTH) AF: 0.252 AC: 15180 AN: 60184

GnomAD4 genome AF: 0.201 AC: 30588 AN: 152174 Hom.: 3916 Cov.: 33 AF XY: 0.203 AC XY: 15137 AN XY: 74386

African (AFR) AF: 0.0463 AC: 1926 AN: 41564

American (AMR) AF: 0.241 AC: 3686 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2445 AN: 5174

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4826

European-Finnish (FIN) AF: 0.283 AC: 2996 AN: 10570

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16819 AN: 67970

Other (OTH) AF: 0.203 AC: 427 AN: 2106

Alfa AF: 0.218 Hom.: 949

Bravo AF: 0.198

Asia WGS AF: 0.301 AC: 1044 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs3826740; hg19: chr19-8032432; COSMIC: COSV60969493;