rs17466502

Variant names:

• chr18-5417184-A-C
• rs17466502
• NM_012307.5:c.1507-806T>G

Your query was ambiguous. Multiple possible variants found:

• chr18-5417184-A-C
• chr18-5417184-A-G

Variant summary

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

The NM_012307.5(EPB41L3):​c.1507-806T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,282 control chromosomes in the GnomAD database, including 1,273 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 0.12 (1273 hom., cov: 32)
• Consequence: EPB41L3 NM_012307.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 4 publications found

Genes affected

EPB41L3 (HGNC:3380): (erythrocyte membrane protein band 4.1 like 3) Predicted to enable cytoskeletal protein-membrane anchor activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in several processes, including nervous system development; paranodal junction maintenance; and protein localization to paranode region of axon. Located in cell-cell junction and plasma membrane. Biomarker of meningioma. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012307.5. 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
	EPB41L3	NM_012307.5	MANE Select	c.1507-806T>G		intron	N/A	NP_036439.2
	EPB41L3	NM_001384685.1		c.1561-806T>G		intron	N/A	NP_001371614.1
	EPB41L3	NM_001330557.2		c.1560+2527T>G		intron	N/A	NP_001317486.1	A0A0A0MRA8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPB41L3	ENST00000341928.7	TSL:1 MANE Select	c.1507-806T>G		intron	N/A	ENSP00000343158.2	Q9Y2J2-1
	EPB41L3	ENST00000540638.6	TSL:1	c.1560+2527T>G		intron	N/A	ENSP00000442091.2	Q9Y2J2-2
	EPB41L3	ENST00000866153.1		c.1560+2527T>G		intron	N/A	ENSP00000536212.1

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18416 AN: 152164 Hom.: 1277 Cov.: 32

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.121 AC: 18402 AN: 152282 Hom.: 1273 Cov.: 32 AF XY: 0.119 AC XY: 8874 AN XY: 74452

African (AFR) AF: 0.0548 AC: 2278 AN: 41550

American (AMR) AF: 0.154 AC: 2352 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3472

East Asian (EAS) AF: 0.113 AC: 585 AN: 5188

South Asian (SAS) AF: 0.121 AC: 583 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1339 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10168 AN: 68030

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.136 Hom.: 3045

Bravo AF: 0.123

Asia WGS AF: 0.118 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.3
DANN	Benign	0.66
PhyloP100		1.2
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: rs17466502; hg19: chr18-5417183;