rs2160430

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014800.11(ELMO1):​c.1086+27590A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,000 control chromosomes in the GnomAD database, including 41,832 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 ( 41832 hom., cov: 31)

Consequence

ELMO1
NM_014800.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ELMO1NM_014800.11 linkuse as main transcriptc.1086+27590A>G intron_variant ENST00000310758.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ELMO1ENST00000310758.9 linkuse as main transcriptc.1086+27590A>G intron_variant 1 NM_014800.11 P1Q92556-1

Frequencies

GnomAD3 genomes
AF:
0.740
AC:
112428
AN:
151882
Hom.:
41814
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.669
Gnomad AMI
AF:
0.811
Gnomad AMR
AF:
0.762
Gnomad ASJ
AF:
0.734
Gnomad EAS
AF:
0.760
Gnomad SAS
AF:
0.869
Gnomad FIN
AF:
0.786
Gnomad MID
AF:
0.706
Gnomad NFE
AF:
0.761
Gnomad OTH
AF:
0.726
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.740
AC:
112492
AN:
152000
Hom.:
41832
Cov.:
31
AF XY:
0.744
AC XY:
55259
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.669
Gnomad4 AMR
AF:
0.762
Gnomad4 ASJ
AF:
0.734
Gnomad4 EAS
AF:
0.760
Gnomad4 SAS
AF:
0.867
Gnomad4 FIN
AF:
0.786
Gnomad4 NFE
AF:
0.761
Gnomad4 OTH
AF:
0.729
Alfa
AF:
0.754
Hom.:
71912
Bravo
AF:
0.732
Asia WGS
AF:
0.800
AC:
2782
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.85
DANN
Benign
0.75

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2160430; hg19: chr7-37223401; API