20-46368695-GC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_133171.5(ELMO2):c.1962+195del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.84 (55572 hom., cov: 0)
• Consequence: ELMO2 NM_133171.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.27

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 -10 ACMG points.

• BP6: Variant 20-46368695-GC-G is Benign according to our data. Variant chr20-46368695-GC-G is described in ClinVar as [Benign]. Clinvar id is 1222840.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO2	NM_133171.5	c.1962+195del		intron_variant		ENST00000290246.11
LOC124904917	XR_007067614.1	n.182+3982del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO2	ENST00000290246.11	c.1962+195del		intron_variant		1	NM_133171.5	P4
	ENST00000651935.1	n.151+3982del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128382 AN: 151962 Hom.: 55551 Cov.: 0

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.859

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.845 AC: 128447 AN: 152080 Hom.: 55572 Cov.: 0 AF XY: 0.850 AC XY: 63209 AN XY: 74364

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.860

Alfa AF: 0.889 Hom.: 7446

Bravo AF: 0.831

Asia WGS AF: 0.851 AC: 2957 AN: 3474

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

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: rs3092402; hg19: chr20-44997334;