Variant rs78699431 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The XM_054328428.1(LOC124900416):c.211_212insTGAGG(p.Ter71LeufsTer8) variant causes a frameshift, stop lost, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000743 in 1,345,258 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 20)

Exomes 𝑓: 7.4e-7 ( 0 hom. )

Consequence

LOC124900416
XM_054328428.1 frameshift, stop_lost, splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Variant links:

Genes affected

EFCAB2 (HGNC:28166): (EF-hand calcium binding domain 2) The gene encodes a protein that contains two EF-hand calcium-binding domains although its function has yet to be determined. Alternatively spliced transcripts have been observed. [provided by RefSeq, Mar 2014]

EFCAB2 links:

LOC124900416 (HGNC:):

LOC124900416 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Stoplost variant in XM_054328428.1 Downstream stopcodon found after 301 codons.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
EFCAB2	NM_032328.4 linkuse as main transcript	c.-90-3_-90-2insCCTCA		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000366523.6	NP_115704.1
LOC124900416	XM_054328428.1 linkuse as main transcript	c.211_212insTGAGG	p.Ter71LeufsTer8	frameshift_variant, stop_lost, splice_region_variant, intron_variant	1/4		XP_054184403.1
LOC101928068	NR_111907.1 linkuse as main transcript	n.59-348_59-347insTGAGG		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB2	ENST00000366523.6 linkuse as main transcript	c.-90-3_-90-2insCCTCA		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		3	NM_032328.4	ENSP00000355480	P1	Q5VUJ9-2
	ENST00000607453.1 linkuse as main transcript	n.762_763insTGAGG		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

7.43e-7

AC:

AN:

1345258

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

665630

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.54e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over