14-88642434-G-A

Variant names:

• chr14-88642434-G-A
• rs11159863
• NM_183387.3:c.4237+459C>T

Variant summary

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

The NM_183387.3(EML5):​c.4237+459C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,980 control chromosomes in the GnomAD database, including 3,321 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 0.19 (3321 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 6 publications found

Genes affected

EML5 (HGNC:18197): (EMAP like 5) Predicted to enable microtubule binding activity. Located in extracellular exosome. [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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183387.3. 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
	EML5	NM_183387.3	MANE Select	c.4237+459C>T		intron	N/A	NP_899243.1	Q05BV3-5
	EML5	NM_001385116.1		c.4228+459C>T		intron	N/A	NP_001372045.1
	EML5	NM_001411033.1		c.4213+459C>T		intron	N/A	NP_001397962.1	Q05BV3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EML5	ENST00000554922.6	TSL:5 MANE Select	c.4237+459C>T		intron	N/A	ENSP00000451998.1	Q05BV3-5
	EML5	ENST00000380664.9	TSL:5	c.4213+459C>T		intron	N/A	ENSP00000370039.5	Q05BV3-1
	EML5	ENST00000971666.1		c.4099+459C>T		intron	N/A	ENSP00000641725.1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29127 AN: 151862 Hom.: 3310 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.192 AC: 29170 AN: 151980 Hom.: 3321 Cov.: 32 AF XY: 0.197 AC XY: 14640 AN XY: 74282

African (AFR) AF: 0.187 AC: 7767 AN: 41474

American (AMR) AF: 0.325 AC: 4955 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2424 AN: 5162

South Asian (SAS) AF: 0.170 AC: 818 AN: 4820

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10572

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10051 AN: 67920

Other (OTH) AF: 0.214 AC: 451 AN: 2110

Alfa AF: 0.168 Hom.: 1957

Bravo AF: 0.212

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.18
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: rs11159863; hg19: chr14-89108778;