15-30371143-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_139320.2(CHRFAM7A):c.565G>A(p.Val189Met) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_139320.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRFAM7A | ENST00000299847.7 | c.565G>A | p.Val189Met | missense_variant | Exon 8 of 10 | 1 | NM_139320.2 | ENSP00000299847.3 | ||
CHRFAM7A | ENST00000401522.7 | c.292G>A | p.Val98Met | missense_variant | Exon 9 of 11 | 1 | ENSP00000385389.3 | |||
CHRFAM7A | ENST00000397827.7 | c.292G>A | p.Val98Met | missense_variant | Exon 7 of 9 | 5 | ENSP00000380927.3 | |||
CHRFAM7A | ENST00000692430.1 | n.517G>A | non_coding_transcript_exon_variant | Exon 3 of 5 |
Frequencies
GnomAD3 genomes AF: 0.0000742 AC: 11AN: 148212Hom.: 0 Cov.: 24
GnomAD3 exomes AF: 0.0000217 AC: 5AN: 230396Hom.: 0 AF XY: 0.00000802 AC XY: 1AN XY: 124736
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000463 AC: 65AN: 1402812Hom.: 0 Cov.: 27 AF XY: 0.0000414 AC XY: 29AN XY: 700034
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000742 AC: 11AN: 148212Hom.: 0 Cov.: 24 AF XY: 0.000111 AC XY: 8AN XY: 72294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.565G>A (p.V189M) alteration is located in exon 8 (coding exon 6) of the CHRFAM7A gene. This alteration results from a G to A substitution at nucleotide position 565, causing the valine (V) at amino acid position 189 to be replaced by a methionine (M). 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