chr1-63568421-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032437.4(EFCAB7):c.1609C>A(p.Leu537Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,434,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032437.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFCAB7 | NM_032437.4 | c.1609C>A | p.Leu537Ile | missense_variant | 12/14 | ENST00000371088.5 | |
EFCAB7 | XM_006710976.4 | c.1648C>A | p.Leu550Ile | missense_variant | 12/14 | ||
EFCAB7 | XM_006710977.2 | c.1609C>A | p.Leu537Ile | missense_variant | 12/14 | ||
EFCAB7 | XM_011542301.3 | c.1648C>A | p.Leu550Ile | missense_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB7 | ENST00000371088.5 | c.1609C>A | p.Leu537Ile | missense_variant | 12/14 | 1 | NM_032437.4 | P1 | |
EFCAB7 | ENST00000460678.6 | n.891C>A | non_coding_transcript_exon_variant | 6/7 | 5 | ||||
EFCAB7 | ENST00000461039.1 | n.836C>A | non_coding_transcript_exon_variant | 4/5 | 2 | ||||
ITGB3BP | ENST00000478138.1 | n.197+25104G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000838 AC: 19AN: 226610Hom.: 0 AF XY: 0.0000487 AC XY: 6AN XY: 123088
GnomAD4 exome AF: 0.0000174 AC: 25AN: 1434134Hom.: 0 Cov.: 30 AF XY: 0.0000112 AC XY: 8AN XY: 712942
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.1609C>A (p.L537I) alteration is located in exon 12 (coding exon 11) of the EFCAB7 gene. This alteration results from a C to A substitution at nucleotide position 1609, causing the leucine (L) at amino acid position 537 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at