dbSNP rs9969311: ELMO1:c.-73-32691C>T (chr7-37375454-G-A) – 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.-73-32691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 655,996 control chromosomes in the GnomAD database, including 16,901 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 0.18 ( 3011 hom., cov: 32)

Exomes 𝑓: 0.19 ( 13890 hom. )

Consequence

ELMO1
NM_014800.11 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71

Publications

8 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 links:

RPS10P14 (HGNC:35880): (ribosomal protein S10 pseudogene 14)

RPS10P14 links:

Genome browser will be placed here

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=-1.04).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11 link	c.-73-32691C>T		intron_variant	Intron 1 of 21	ENST00000310758.9	NP_055615.8	Q92556-1A4D1X5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9 link	c.-73-32691C>T		intron_variant	Intron 1 of 21	1	NM_014800.11	ENSP00000312185.4		Q92556-1

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26750

AN:

151964

Hom.:

3003

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.135

Gnomad EAS

AF:

0.587

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.186

GnomAD4 exome

AF:

0.193

AC:

97131

AN:

503914

Hom.:

13890

AF XY:

0.197

AC XY:

52988

AN XY:

268924

show subpopulations

African (AFR)

AF:

0.174

AC:

2543

AN:

14612

American (AMR)

AF:

0.333

AC:

10067

AN:

30274

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

2208

AN:

16240

East Asian (EAS)

AF:

0.605

AC:

18965

AN:

31322

South Asian (SAS)

AF:

0.305

AC:

16219

AN:

53216

European-Finnish (FIN)

AF:

0.171

AC:

5433

AN:

31746

Middle Eastern (MID)

AF:

0.194

AC:

412

AN:

2124

European-Non Finnish (NFE)

AF:

0.122

AC:

36295

AN:

296342

Other (OTH)

AF:

0.178

AC:

4989

AN:

28038

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3502

7004

10506

14008

17510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

464

928

1392

1856

2320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.176

AC:

26788

AN:

152082

Hom.:

3011

Cov.:

AF XY:

0.185

AC XY:

13742

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.176

AC:

7317

AN:

41502

American (AMR)

AF:

0.248

AC:

3797

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.135

AC:

469

AN:

3468

East Asian (EAS)

AF:

0.587

AC:

3029

AN:

5158

South Asian (SAS)

AF:

0.295

AC:

1414

AN:

4794

European-Finnish (FIN)

AF:

0.173

AC:

1829

AN:

10586

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8335

AN:

67972

Other (OTH)

AF:

0.189

AC:

398

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1060

2121

3181

4242

5302

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.0975

Hom.:

207

Bravo

AF:

0.185

Asia WGS

AF:

0.406

AC:

1408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.67

(source)

DANN

Benign

0.56

PhyloP100

-1.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over