18-2874158-G-A

Position:

• chr18-2874158-G-A

Variant summary

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

The NM_032048.3(EMILIN2):​c.258-10806G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,002 control chromosomes in the GnomAD database, including 32,150 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 0.65 (32150 hom., cov: 32)
• Consequence: EMILIN2 NM_032048.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

Genes affected

EMILIN2 (HGNC:19881): (elastin microfibril interfacer 2) Predicted to enable extracellular matrix constituent conferring elasticity. Predicted to be involved in cell adhesion. Located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EMILIN2	NM_032048.3	c.258-10806G>A		intron_variant		ENST00000254528.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EMILIN2	ENST00000254528.4	c.258-10806G>A		intron_variant		1	NM_032048.3	P1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98168 AN: 151884 Hom.: 32120 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.646 AC: 98244 AN: 152002 Hom.: 32150 Cov.: 32 AF XY: 0.640 AC XY: 47599 AN XY: 74328

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.656

Alfa AF: 0.675 Hom.: 45935

Bravo AF: 0.638

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.55

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: rs583523; hg19: chr18-2874156;