NM_153702.4:c.533+167T>C

Variant names:

• chr4-140540468-T-C
• rs74288616
• NM_153702.4:c.533+167T>C

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.533+167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,202 control chromosomes in the GnomAD database, including 2,964 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (2964 hom., cov: 32)
• Consequence: ELMOD2 NM_153702.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.386

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=-0.86).
• BP6: Variant 4-140540468-T-C is Benign according to our data. Variant chr4-140540468-T-C is described in ClinVar as [Benign]. Clinvar id is 1265510.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMOD2	NM_153702.4	c.533+167T>C		intron_variant	Intron 6 of 8	ENST00000323570.8	NP_714913.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMOD2	ENST00000323570.8	c.533+167T>C		intron_variant	Intron 6 of 8	1	NM_153702.4	ENSP00000326342.3
ELMOD2	ENST00000512057.1	n.678+167T>C		intron_variant	Intron 3 of 4	5
ELMOD2	ENST00000502397.5	c.*197T>C		downstream_gene_variant		5		ENSP00000422582.1
ELMOD2	ENST00000513606.1	c.*179T>C		downstream_gene_variant		4		ENSP00000427592.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29555 AN: 152084 Hom.: 2965 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.194 AC: 29579 AN: 152202 Hom.: 2964 Cov.: 32 AF XY: 0.196 AC XY: 14605 AN XY: 74438

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.193

Alfa AF: 0.184 Hom.: 339

Bravo AF: 0.201

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs74288616; hg19: chr4-141461622;