rs10132509

Variant names:

• chr14-88737437-A-G
• rs10132509
• NM_183387.3:c.848-872T>C

Variant summary

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

The NM_183387.3(EML5):​c.848-872T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,134 control chromosomes in the GnomAD database, including 35,896 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 0.67 (35896 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EML5	NM_183387.3	MANE Select	c.848-872T>C		intron	N/A	NP_899243.1
	EML5	NM_001385116.1		c.848-872T>C		intron	N/A	NP_001372045.1
	EML5	NM_001411033.1		c.848-872T>C		intron	N/A	NP_001397962.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EML5	ENST00000554922.6	TSL:5 MANE Select	c.848-872T>C		intron	N/A	ENSP00000451998.1
	EML5	ENST00000380664.9	TSL:5	c.848-872T>C		intron	N/A	ENSP00000370039.5

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101067 AN: 152016 Hom.: 35815 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.665 AC: 101210 AN: 152134 Hom.: 35896 Cov.: 32 AF XY: 0.665 AC XY: 49457 AN XY: 74372

African (AFR) AF: 0.897 AC: 37254 AN: 41552

American (AMR) AF: 0.669 AC: 10241 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4849 AN: 5138

South Asian (SAS) AF: 0.752 AC: 3626 AN: 4822

European-Finnish (FIN) AF: 0.493 AC: 5211 AN: 10578

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36079 AN: 67962

Other (OTH) AF: 0.618 AC: 1305 AN: 2112

Alfa AF: 0.593 Hom.: 6753

Bravo AF: 0.690

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		-0.50
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: rs10132509; hg19: chr14-89203781;