chr5-160229619-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001445.3(FABP6):c.62T>A(p.Leu21His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00276 in 1,613,704 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L21L) has been classified as Benign.
Frequency
Consequence
NM_001445.3 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 |
---|---|---|---|---|---|---|---|
FABP6 | NM_001445.3 | c.62T>A | p.Leu21His | missense_variant | 1/4 | ENST00000402432.4 | |
FABP6 | NM_001040442.1 | c.209T>A | p.Leu70His | missense_variant | 3/6 | ||
FABP6 | NM_001130958.2 | c.209T>A | p.Leu70His | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FABP6 | ENST00000402432.4 | c.62T>A | p.Leu21His | missense_variant | 1/4 | 1 | NM_001445.3 | P1 | |
FABP6 | ENST00000393980.8 | c.209T>A | p.Leu70His | missense_variant | 4/7 | 1 | |||
FABP6 | ENST00000523955.5 | c.*270T>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0151 AC: 2291AN: 152024Hom.: 63 Cov.: 32
GnomAD3 exomes AF: 0.00383 AC: 963AN: 251234Hom.: 21 AF XY: 0.00264 AC XY: 359AN XY: 135782
GnomAD4 exome AF: 0.00148 AC: 2158AN: 1461562Hom.: 49 Cov.: 30 AF XY: 0.00125 AC XY: 908AN XY: 727102
GnomAD4 genome ? AF: 0.0150 AC: 2289AN: 152142Hom.: 63 Cov.: 32 AF XY: 0.0145 AC XY: 1080AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at