14-88765501-T-C

Variant names:

• chr14-88765501-T-C
• rs7157149
• NM_183387.3:c.198-10830A>G

Variant summary

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

The NM_183387.3(EML5):​c.198-10830A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,116 control chromosomes in the GnomAD database, including 4,642 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 0.24 (4642 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 5 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 = 0.361 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.198-10830A>G		intron	N/A	NP_899243.1
	EML5	NM_001385116.1		c.198-10830A>G		intron	N/A	NP_001372045.1
	EML5	NM_001411033.1		c.198-10830A>G		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.198-10830A>G		intron	N/A	ENSP00000451998.1
	EML5	ENST00000380664.9	TSL:5	c.198-10830A>G		intron	N/A	ENSP00000370039.5

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36812 AN: 151996 Hom.: 4630 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.242 AC: 36861 AN: 152116 Hom.: 4642 Cov.: 32 AF XY: 0.240 AC XY: 17838 AN XY: 74358

African (AFR) AF: 0.212 AC: 8813 AN: 41484

American (AMR) AF: 0.224 AC: 3417 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1944 AN: 5180

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4828

European-Finnish (FIN) AF: 0.235 AC: 2477 AN: 10562

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17487 AN: 67994

Other (OTH) AF: 0.217 AC: 457 AN: 2110

Alfa AF: 0.247 Hom.: 793

Bravo AF: 0.241

Asia WGS AF: 0.286 AC: 992 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	9.0
DANN	Benign	0.94
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs7157149; hg19: chr14-89231845;