rs10140896

Variant names:

• chr14-88752194-C-A
• rs10140896
• NM_183387.3:c.357+2318G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-88752194-C-A
• chr14-88752194-C-G
• chr14-88752194-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_183387.3(EML5):​c.357+2318G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00281 in 152,044 control chromosomes in the GnomAD database, including 3 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 0.0028 (3 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 9 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

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.357+2318G>T		intron	N/A	NP_899243.1	Q05BV3-5
	EML5	NM_001385116.1		c.357+2318G>T		intron	N/A	NP_001372045.1
	EML5	NM_001411033.1		c.357+2318G>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.357+2318G>T		intron	N/A	ENSP00000451998.1	Q05BV3-5
	EML5	ENST00000380664.9	TSL:5	c.357+2318G>T		intron	N/A	ENSP00000370039.5	Q05BV3-1
	EML5	ENST00000971666.1		c.357+2318G>T		intron	N/A	ENSP00000641725.1

Frequencies

GnomAD3 genomes AF: 0.00282 AC: 429 AN: 151926 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00988

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000787

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00335

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

GnomAD4 genome AF: 0.00281 AC: 428 AN: 152044 Hom.: 3 Cov.: 32 AF XY: 0.00269 AC XY: 200 AN XY: 74310

African (AFR) AF: 0.00985 AC: 409 AN: 41508

American (AMR) AF: 0.000786 AC: 12 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10540

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67942

Other (OTH) AF: 0.00332 AC: 7 AN: 2110

Alfa AF: 0.00 Hom.: 906

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.59
PhyloP100		-0.45

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: rs10140896; hg19: chr14-89218538;