rs78699431

Variant names:

• chr1-244970326-C-CCCTCA
• NM_032328.4:c.-90-3_-90-2insCCTCA

Your query was ambiguous. Multiple possible variants found:

• chr1-244970326-C-CCCTCA
• chr1-244970326-C-CCCTCG
• chr1-244970326-C-CCCTCT

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Strong PM2

The NM_032328.4(EFCAB2):​c.-90-3_-90-2insCCTCA variant causes a splice acceptor, 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: EFCAB2 NM_032328.4 splice_acceptor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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]

LOC124900416 (HGNC:):

ENSG00000272195 (HGNC:58101):

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.23517382 fraction of the gene. Cryptic splice site detected, with MaxEntScore 6.9, offset of 0 (no position change), new splice context is: cggcccctcctcccctcaAGgcc. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB2	NM_032328.4	c.-90-3_-90-2insCCTCA		splice_acceptor_variant, intron_variant	Intron 1 of 7	ENST00000366523.6	NP_115704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB2	ENST00000366523.6	c.-90-3_-90-2insCCTCA		splice_acceptor_variant, intron_variant	Intron 1 of 7	3	NM_032328.4	ENSP00000355480.1

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome AF: 7.43e-7 AC: 1 AN: 1345258 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 665630

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.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-245133628;