NM_183387.3:c.3125-2527G>A

Variant names:

• chr14-88668016-C-T
• rs1956411
• NM_183387.3:c.3125-2527G>A

Variant summary

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

The NM_183387.3(EML5):​c.3125-2527G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,052 control chromosomes in the GnomAD database, including 34,092 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 0.65 (34092 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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.3125-2527G>A		intron	N/A	NP_899243.1	Q05BV3-5
	EML5	NM_001385116.1		c.3125-2527G>A		intron	N/A	NP_001372045.1
	EML5	NM_001411033.1		c.3125-2527G>A		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.3125-2527G>A		intron	N/A	ENSP00000451998.1	Q05BV3-5
	EML5	ENST00000380664.9	TSL:5	c.3125-2527G>A		intron	N/A	ENSP00000370039.5	Q05BV3-1
	EML5	ENST00000971666.1		c.3011-2527G>A		intron	N/A	ENSP00000641725.1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98768 AN: 151934 Hom.: 34024 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.650 AC: 98890 AN: 152052 Hom.: 34092 Cov.: 32 AF XY: 0.648 AC XY: 48158 AN XY: 74288

African (AFR) AF: 0.865 AC: 35913 AN: 41520

American (AMR) AF: 0.666 AC: 10176 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3468

East Asian (EAS) AF: 0.937 AC: 4847 AN: 5174

South Asian (SAS) AF: 0.677 AC: 3259 AN: 4816

European-Finnish (FIN) AF: 0.474 AC: 4991 AN: 10538

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35772 AN: 67946

Other (OTH) AF: 0.594 AC: 1253 AN: 2110

Alfa AF: 0.612 Hom.: 5302

Bravo AF: 0.677

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.79
DANN	Benign	0.32
PhyloP100		-0.82
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: rs1956411; hg19: chr14-89134360;