4-140537331-T-G

Variant summary

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

The NM_153702.4(ELMOD2):c.270-81T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 1,224,476 control chromosomes in the GnomAD database, including 270,707 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.56 (25445 hom., cov: 31)
  • Exomes 𝑓: 0.67 (245262 hom.)
• Consequence: ELMOD2 NM_153702.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.217

Genes affected

ELMOD2 (HGNC:28111): (ELMO domain containing 2) This gene encodes one of six engulfment and motility (ELMO) domain-containing proteins. This gene is thought to play a role in antiviral responses. Mutations in this gene may be involved in the cause of familial idiopathic pulmonary fibrosis. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 4-140537331-T-G is Benign according to our data. Variant chr4-140537331-T-G is described in ClinVar as [Benign]. Clinvar id is 1235399.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMOD2	NM_153702.4	c.270-81T>G		intron_variant		ENST00000323570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMOD2	ENST00000323570.8	c.270-81T>G		intron_variant		1	NM_153702.4	P1
ELMOD2	ENST00000502397.5	c.270-81T>G		intron_variant		5
ELMOD2	ENST00000513606.1	c.39-81T>G		intron_variant		4
ELMOD2	ENST00000512057.1	n.415-81T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84416 AN: 151852 Hom.: 25440 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.574

GnomAD4 exome AF: 0.671 AC: 719894 AN: 1072506 Hom.: 245262 AF XY: 0.669 AC XY: 352333 AN XY: 526828

Gnomad4 AFR exome AF: 0.295

Gnomad4 AMR exome AF: 0.562

Gnomad4 ASJ exome AF: 0.643

Gnomad4 EAS exome AF: 0.539

Gnomad4 SAS exome AF: 0.528

Gnomad4 FIN exome AF: 0.670

Gnomad4 NFE exome AF: 0.696

Gnomad4 OTH exome AF: 0.641

GnomAD4 genome AF: 0.556 AC: 84453 AN: 151970 Hom.: 25445 Cov.: 31 AF XY: 0.552 AC XY: 40994 AN XY: 74278

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.574

Alfa AF: 0.602 Hom.: 4297

Bravo AF: 0.538

Asia WGS AF: 0.481 AC: 1669 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

Nov 11, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	14
Dann	Benign	0.86

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: rs882930; hg19: chr4-141458485;