rs637647

Variant names:

• chr18-2881841-T-C
• rs637647
• NM_032048.3:c.258-3123T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032048.3(EMILIN2):​c.258-3123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,158 control chromosomes in the GnomAD database, including 38,503 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 0.70 (38503 hom., cov: 34)
• Consequence: EMILIN2 NM_032048.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMILIN2	NM_032048.3	c.258-3123T>C		intron_variant	Intron 2 of 7	ENST00000254528.4	NP_114437.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMILIN2	ENST00000254528.4	c.258-3123T>C		intron_variant	Intron 2 of 7	1	NM_032048.3	ENSP00000254528.3

Frequencies

GnomAD3 genomes AF: 0.704 AC: 107003 AN: 152040 Hom.: 38480 Cov.: 34

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.704 AC: 107074 AN: 152158 Hom.: 38503 Cov.: 34 AF XY: 0.701 AC XY: 52156 AN XY: 74394

African (AFR) AF: 0.631 AC: 26181 AN: 41496

American (AMR) AF: 0.659 AC: 10063 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2208 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1677 AN: 5166

South Asian (SAS) AF: 0.719 AC: 3471 AN: 4828

European-Finnish (FIN) AF: 0.804 AC: 8529 AN: 10608

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52584 AN: 67998

Other (OTH) AF: 0.669 AC: 1413 AN: 2112

Alfa AF: 0.746 Hom.: 177425

Bravo AF: 0.685

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.43
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs637647; hg19: chr18-2881839;