20-46367615-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_133171.5(ELMO2):c.1963-55G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 1,455,170 control chromosomes in the GnomAD database, including 7,663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (2127 hom., cov: 32)
  • Exomes 𝑓: 0.082 (5536 hom.)
• Consequence: ELMO2 NM_133171.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.490

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP6: Variant 20-46367615-C-A is Benign according to our data. Variant chr20-46367615-C-A is described in ClinVar as [Benign]. Clinvar id is 1269238.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO2	NM_133171.5	c.1963-55G>T		intron_variant		ENST00000290246.11
LOC124904917	XR_007067614.1	n.182+2895C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO2	ENST00000290246.11	c.1963-55G>T		intron_variant		1	NM_133171.5	P4
	ENST00000651935.1	n.151+2895C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20381 AN: 151968 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.0815 AC: 106204 AN: 1303082 Hom.: 5536 AF XY: 0.0807 AC XY: 52081 AN XY: 645624

Gnomad4 AFR exome AF: 0.298

Gnomad4 AMR exome AF: 0.0730

Gnomad4 ASJ exome AF: 0.0587

Gnomad4 EAS exome AF: 0.195

Gnomad4 SAS exome AF: 0.0819

Gnomad4 FIN exome AF: 0.0410

Gnomad4 NFE exome AF: 0.0733

Gnomad4 OTH exome AF: 0.0948

GnomAD4 genome AF: 0.134 AC: 20422 AN: 152088 Hom.: 2127 Cov.: 32 AF XY: 0.130 AC XY: 9661 AN XY: 74350

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0914

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0904

Gnomad4 FIN AF: 0.0388

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.125

Alfa AF: 0.105 Hom.: 238

Bravo AF: 0.145

Asia WGS AF: 0.144 AC: 502 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 12, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	14
Dann	Benign	0.87

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

Other links and lift over

dbSNP: rs2297058; hg19: chr20-44996254;