2-27079297-T-C

Variant names:

• chr2-27079297-T-C
• rs2289360
• NM_007046.4:c.170+62T>C

Variant summary

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

The NM_007046.4(EMILIN1):​c.170+62T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 1,371,956 control chromosomes in the GnomAD database, including 265,064 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 0.56 (24686 hom., cov: 33)
  • Exomes 𝑓: 0.62 (240378 hom.)
• Consequence: EMILIN1 NM_007046.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.64

Genes affected

EMILIN1 (HGNC:19880): (elastin microfibril interfacer 1) This gene encodes an extracellular matrix glycoprotein that is characterized by an N-terminal microfibril interface domain, a coiled-coiled alpha-helical domain, a collagenous domain and a C-terminal globular C1q domain. The encoded protein associates with elastic fibers at the interface between elastin and microfibrils and may play a role in the development of elastic tissues including large blood vessels, dermis, heart and lung. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMILIN1	NM_007046.4	c.170+62T>C		intron_variant	Intron 1 of 7	ENST00000380320.9	NP_008977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMILIN1	ENST00000380320.9	c.170+62T>C		intron_variant	Intron 1 of 7	1	NM_007046.4	ENSP00000369677.4

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85121 AN: 152004 Hom.: 24672 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 0.624 AC: 761618 AN: 1219834 Hom.: 240378 AF XY: 0.626 AC XY: 378186 AN XY: 604208

Gnomad4 AFR exome AF: 0.425

Gnomad4 AMR exome AF: 0.403

Gnomad4 ASJ exome AF: 0.601

Gnomad4 EAS exome AF: 0.783

Gnomad4 SAS exome AF: 0.681

Gnomad4 FIN exome AF: 0.651

Gnomad4 NFE exome AF: 0.624

Gnomad4 OTH exome AF: 0.619

GnomAD4 genome AF: 0.560 AC: 85150 AN: 152122 Hom.: 24686 Cov.: 33 AF XY: 0.562 AC XY: 41804 AN XY: 74382

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.573

Alfa AF: 0.568 Hom.: 3580

Bravo AF: 0.534

Asia WGS AF: 0.682 AC: 2372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.019
DANN	Benign	0.45

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: rs2289360; hg19: chr2-27302165;