chr1-63533523-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032437.4(EFCAB7):āc.556A>Gā(p.Ser186Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,613,414 control chromosomes in the GnomAD database, including 48 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 (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
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.556A>G | p.Ser186Gly | missense_variant | 5/14 | ENST00000371088.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB7 | ENST00000371088.5 | c.556A>G | p.Ser186Gly | missense_variant | 5/14 | 1 | NM_032437.4 | P1 | |
ITGB3BP | ENST00000478138.1 | n.198-4337T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00989 AC: 1504AN: 152146Hom.: 23 Cov.: 32
GnomAD3 exomes AF: 0.00254 AC: 638AN: 250770Hom.: 10 AF XY: 0.00187 AC XY: 254AN XY: 135574
GnomAD4 exome AF: 0.00109 AC: 1594AN: 1461150Hom.: 25 Cov.: 31 AF XY: 0.000930 AC XY: 676AN XY: 726912
GnomAD4 genome AF: 0.00988 AC: 1505AN: 152264Hom.: 23 Cov.: 32 AF XY: 0.00908 AC XY: 676AN XY: 74458
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