chr2-55885305-C-A

Position:

• chr2-55885305-C-A

Variant summary

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

The NM_001039348.3(EFEMP1):​c.518-3571G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,014 control chromosomes in the GnomAD database, including 24,201 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 0.54 (24201 hom., cov: 32)
• Consequence: EFEMP1 NM_001039348.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

EFEMP1 (HGNC:3218): (EGF containing fibulin extracellular matrix protein 1) This gene encodes a member of the fibulin family of extracellular matrix glycoproteins. Like all members of this family, the encoded protein contains tandemly repeated epidermal growth factor-like repeats followed by a C-terminus fibulin-type domain. This gene is upregulated in malignant gliomas and may play a role in the aggressive nature of these tumors. Mutations in this gene are associated with Doyne honeycomb retinal dystrophy. Alternatively spliced transcript variants that encode the same protein have been described.[provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFEMP1	NM_001039348.3	c.518-3571G>T		intron_variant		ENST00000355426.8
EFEMP1	NM_001039349.3	c.518-3571G>T		intron_variant
EFEMP1	XM_005264205.5	c.518-3571G>T		intron_variant
EFEMP1	XM_017003586.3	c.518-3571G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFEMP1	ENST00000355426.8	c.518-3571G>T		intron_variant		1	NM_001039348.3	P1
EFEMP1	ENST00000394555.6	c.518-3571G>T		intron_variant		1		P1
EFEMP1	ENST00000634374.1	c.117-3571G>T		intron_variant		5
EFEMP1	ENST00000635671.1	c.*410-3571G>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82558 AN: 151896 Hom.: 24168 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.544 AC: 82642 AN: 152014 Hom.: 24201 Cov.: 32 AF XY: 0.546 AC XY: 40601 AN XY: 74304

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.561

Alfa AF: 0.487 Hom.: 9350

Bravo AF: 0.553

Asia WGS AF: 0.761 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
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: rs1367228; hg19: chr2-56112440;