rs1430197

chr2-55907692-G-Achr2-55907692-G-Cchr2-55907692-G-T

Variant summary

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

The NM_001039348.3(EFEMP1):c.517+9973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,042 control chromosomes in the GnomAD database, including 13,383 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 0.41 (13383 hom., cov: 32)
• Consequence: EFEMP1 NM_001039348.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFEMP1	NM_001039348.3	c.517+9973C>T		intron_variant		ENST00000355426.8
EFEMP1	NM_001039349.3	c.517+9973C>T		intron_variant
EFEMP1	XM_005264205.5	c.517+9973C>T		intron_variant
EFEMP1	XM_017003586.3	c.517+9973C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFEMP1	ENST00000355426.8	c.517+9973C>T		intron_variant		1	NM_001039348.3	P1
EFEMP1	ENST00000394555.6	c.517+9973C>T		intron_variant		1		P1
EFEMP1	ENST00000634374.1	c.116+9973C>T		intron_variant		5
EFEMP1	ENST00000635671.1	c.*409+9973C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62606 AN: 151926 Hom.: 13371 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.412 AC: 62660 AN: 152042 Hom.: 13383 Cov.: 32 AF XY: 0.413 AC XY: 30679 AN XY: 74314

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.414

Alfa AF: 0.365 Hom.: 7972

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.32
Dann	Benign	0.43

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: rs1430197; hg19: chr2-56134827;