20-46369063-C-T

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.1885-95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 1,116,122 control chromosomes in the GnomAD database, including 6,401 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (2133 hom., cov: 32)
  • Exomes 𝑓: 0.081 (4268 hom.)
• Consequence: ELMO2 NM_133171.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.16

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=-0.8).
• BP6: Variant 20-46369063-C-T is Benign according to our data. Variant chr20-46369063-C-T is described in ClinVar as [Benign]. Clinvar id is 1183768.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.1885-95G>A		intron_variant		ENST00000290246.11
LOC124904917	XR_007067614.1	n.182+4343C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO2	ENST00000290246.11	c.1885-95G>A		intron_variant		1	NM_133171.5	P4
	ENST00000651935.1	n.151+4343C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20409 AN: 152018 Hom.: 2124 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.0812 AC: 78257 AN: 963986 Hom.: 4268 Cov.: 13 AF XY: 0.0805 AC XY: 40105 AN XY: 498054

Gnomad4 AFR exome AF: 0.294

Gnomad4 AMR exome AF: 0.0720

Gnomad4 ASJ exome AF: 0.0600

Gnomad4 EAS exome AF: 0.195

Gnomad4 SAS exome AF: 0.0810

Gnomad4 FIN exome AF: 0.0409

Gnomad4 NFE exome AF: 0.0709

Gnomad4 OTH exome AF: 0.0945

GnomAD4 genome AF: 0.134 AC: 20450 AN: 152136 Hom.: 2133 Cov.: 32 AF XY: 0.130 AC XY: 9677 AN XY: 74386

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.0914

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0907

Gnomad4 FIN AF: 0.0388

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.124

Alfa AF: 0.105 Hom.: 296

Bravo AF: 0.146

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	-0.80
Cadd	Benign	1.1
Dann	Benign	0.81

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: rs2297055; hg19: chr20-44997702; COSMIC: COSV51682863; COSMIC: COSV51682863;