chr6-115967662-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002031.3(FRK):c.688G>A(p.Asp230Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000651 in 1,613,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002031.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRK | NM_002031.3 | c.688G>A | p.Asp230Asn | missense_variant | 4/8 | ENST00000606080.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRK | ENST00000606080.2 | c.688G>A | p.Asp230Asn | missense_variant | 4/8 | 1 | NM_002031.3 | P1 | |
ENST00000692859.2 | n.223-65484G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000593 AC: 9AN: 151728Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251312Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135826
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461444Hom.: 0 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727048
GnomAD4 genome AF: 0.0000593 AC: 9AN: 151728Hom.: 0 Cov.: 32 AF XY: 0.0000675 AC XY: 5AN XY: 74050
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.688G>A (p.D230N) alteration is located in exon 4 (coding exon 4) of the FRK gene. This alteration results from a G to A substitution at nucleotide position 688, causing the aspartic acid (D) at amino acid position 230 to be replaced by an asparagine (N). 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