chr1-63571026-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032437.4(EFCAB7):c.1713T>G(p.Asp571Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00273 in 1,601,954 control chromosomes in the GnomAD database, including 108 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_032437.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFCAB7 | NM_032437.4 | c.1713T>G | p.Asp571Glu | missense_variant | 13/14 | ENST00000371088.5 | |
EFCAB7 | XM_006710976.4 | c.1752T>G | p.Asp584Glu | missense_variant | 13/14 | ||
EFCAB7 | XM_006710977.2 | c.1713T>G | p.Asp571Glu | missense_variant | 13/14 | ||
EFCAB7 | XM_011542301.3 | c.1752T>G | p.Asp584Glu | missense_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB7 | ENST00000371088.5 | c.1713T>G | p.Asp571Glu | missense_variant | 13/14 | 1 | NM_032437.4 | P1 | |
EFCAB7 | ENST00000460678.6 | n.995T>G | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
EFCAB7 | ENST00000461039.1 | n.3441T>G | non_coding_transcript_exon_variant | 4/5 | 2 | ||||
ITGB3BP | ENST00000478138.1 | n.197+22499A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0144 AC: 2189AN: 152174Hom.: 47 Cov.: 32
GnomAD3 exomes AF: 0.00388 AC: 941AN: 242638Hom.: 25 AF XY: 0.00293 AC XY: 383AN XY: 130880
GnomAD4 exome AF: 0.00150 AC: 2175AN: 1449662Hom.: 61 Cov.: 28 AF XY: 0.00131 AC XY: 946AN XY: 721062
GnomAD4 genome ? AF: 0.0144 AC: 2196AN: 152292Hom.: 47 Cov.: 32 AF XY: 0.0141 AC XY: 1051AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 25, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at