chr20-46367811-A-G

Position:

• chr20-46367811-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133171.5(ELMO2):​c.1963-251T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,126 control chromosomes in the GnomAD database, including 2,220 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 0.14 (2220 hom., cov: 31)
• Consequence: ELMO2 NM_133171.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO2	NM_133171.5	c.1963-251T>C		intron_variant		ENST00000290246.11	NP_573403.1
LOC124904917	XR_007067614.1	n.182+3091A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELMO2	ENST00000290246.11	c.1963-251T>C		intron_variant		1	NM_133171.5	ENSP00000290246	P4
	ENST00000651935.1	n.151+3091A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20709 AN: 152008 Hom.: 2211 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0907

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.136 AC: 20749 AN: 152126 Hom.: 2220 Cov.: 31 AF XY: 0.132 AC XY: 9813 AN XY: 74366

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0912

Gnomad4 FIN AF: 0.0387

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0798 Hom.: 1276

Bravo AF: 0.148

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.28

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: rs2297056; hg19: chr20-44996450;