Genetic Variant ELMO1:c.1602-1687G>A (chr7-36889359-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014800.11(ELMO1):c.1602-1687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,084 control chromosomes in the GnomAD database, including 42,586 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 0.74 ( 42586 hom., cov: 31)

Consequence

ELMO1
NM_014800.11 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.445

Publications

13 publications found

Variant links:

Genes affected

ELMO1 (HGNC:16286): (engulfment and cell motility 1) This gene encodes a member of the engulfment and cell motility protein family. These proteins interact with dedicator of cytokinesis proteins to promote phagocytosis and cell migration. Increased expression of this gene and dedicator of cytokinesis 1 may promote glioma cell invasion, and single nucleotide polymorphisms in this gene may be associated with diabetic nephropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ELMO1 Gene-Disease associations (from GenCC):

male infertility with azoospermia or oligozoospermia due to single gene mutation
Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center

ELMO1 links:

LOC105375235 (HGNC:):

LOC105375235 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014800.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ELMO1	NM_014800.11	MANE Select	c.1602-1687G>A	intron	N/A	NP_055615.8
ELMO1	NM_001206480.2		c.1602-1687G>A	intron	N/A	NP_001193409.1	A4D1X5
ELMO1	NM_001206482.2		c.1602-1687G>A	intron	N/A	NP_001193411.1	Q92556-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.1602-1687G>A	intron	N/A	ENSP00000312185.4	Q92556-1
ELMO1	ENST00000448602.5	TSL:1	c.1602-1687G>A	intron	N/A	ENSP00000394458.1	Q92556-1
ELMO1	ENST00000396040.6	TSL:1	c.162-1687G>A	intron	N/A	ENSP00000379355.2	Q92556-2

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113163

AN:

151966

Hom.:

42566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.786

Gnomad AMR

AF:

0.677

Gnomad ASJ

AF:

0.810

Gnomad EAS

AF:

0.752

Gnomad SAS

AF:

0.730

Gnomad FIN

AF:

0.787

Gnomad MID

AF:

0.731

Gnomad NFE

AF:

0.810

Gnomad OTH

AF:

0.740

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

GnomAD4 genome

AF:

0.744

AC:

113220

AN:

152084

Hom.:

42586

Cov.:

AF XY:

0.740

AC XY:

55013

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.646

AC:

26770

AN:

41458

American (AMR)

AF:

0.677

AC:

10331

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.810

AC:

2814

AN:

3472

East Asian (EAS)

AF:

0.752

AC:

3877

AN:

5156

South Asian (SAS)

AF:

0.729

AC:

3519

AN:

4824

European-Finnish (FIN)

AF:

0.787

AC:

8342

AN:

10602

Middle Eastern (MID)

AF:

0.724

AC:

213

AN:

294

European-Non Finnish (NFE)

AF:

0.810

AC:

55076

AN:

67990

Other (OTH)

AF:

0.741

AC:

1561

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1459

2919

4378

5838

7297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

856

1712

2568

3424

4280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.787

Hom.:

78064

Bravo

AF:

0.735

Asia WGS

AF:

0.706

AC:

2454

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.70

(source)

DANN

Benign

0.46

PhyloP100

-0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over