20-46369117-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_133171.5(ELMO2):c.1885-149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 682,582 control chromosomes in the GnomAD database, including 6,055 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1118 hom., cov: 32)
  • Exomes 𝑓: 0.13 (4937 hom.)
• Consequence: ELMO2 NM_133171.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.10

Genes affected

ELMO2 (HGNC:17233): (engulfment and cell motility 2) The protein encoded by this gene interacts with the dedicator of cyto-kinesis 1 protein. Similarity to a C. elegans protein suggests that this protein may function in phagocytosis of apoptotic cells and in cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 20-46369117-G-A is Benign according to our data. Variant chr20-46369117-G-A is described in ClinVar as [Benign]. Clinvar id is 1246786.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO2	NM_133171.5	c.1885-149C>T		intron_variant		ENST00000290246.11
LOC124904917	XR_007067614.1	n.182+4397G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO2	ENST00000290246.11	c.1885-149C>T		intron_variant		1	NM_133171.5	P4
	ENST00000651935.1	n.151+4397G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16560 AN: 152124 Hom.: 1118 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0815

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.123

GnomAD4 exome AF: 0.130 AC: 68696 AN: 530340 Hom.: 4937 Cov.: 7 AF XY: 0.129 AC XY: 36088 AN XY: 279306

Gnomad4 AFR exome AF: 0.0460

Gnomad4 AMR exome AF: 0.154

Gnomad4 ASJ exome AF: 0.215

Gnomad4 EAS exome AF: 0.0771

Gnomad4 SAS exome AF: 0.102

Gnomad4 FIN exome AF: 0.0751

Gnomad4 NFE exome AF: 0.142

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.109 AC: 16565 AN: 152242 Hom.: 1118 Cov.: 32 AF XY: 0.106 AC XY: 7882 AN XY: 74428

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0815

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.122

Alfa AF: 0.113 Hom.: 167

Bravo AF: 0.114

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	8.5
Dann	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs41307161; hg19: chr20-44997756;