chr10-15789302-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_024948.4(MINDY3):c.973G>A(p.Asp325Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000584 in 1,610,530 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024948.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MINDY3 | NM_024948.4 | c.973G>A | p.Asp325Asn | missense_variant | Exon 12 of 15 | ENST00000277632.8 | NP_079224.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MINDY3 | ENST00000277632.8 | c.973G>A | p.Asp325Asn | missense_variant | Exon 12 of 15 | 1 | NM_024948.4 | ENSP00000277632.3 | ||
MINDY3 | ENST00000477891.1 | n.1120G>A | non_coding_transcript_exon_variant | Exon 11 of 14 | 1 | |||||
MINDY3 | ENST00000418767.5 | c.493G>A | p.Asp165Asn | missense_variant | Exon 7 of 7 | 3 | ENSP00000388661.1 | |||
MINDY3 | ENST00000378036.5 | c.88G>A | p.Asp30Asn | missense_variant | Exon 3 of 6 | 2 | ENSP00000367275.1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 151802Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 249972Hom.: 1 AF XY: 0.000126 AC XY: 17AN XY: 135158
GnomAD4 exome AF: 0.0000480 AC: 70AN: 1458728Hom.: 1 Cov.: 29 AF XY: 0.0000496 AC XY: 36AN XY: 725738
GnomAD4 genome AF: 0.000158 AC: 24AN: 151802Hom.: 1 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74104
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.973G>A (p.D325N) alteration is located in exon 12 (coding exon 12) of the FAM188A gene. This alteration results from a G to A substitution at nucleotide position 973, causing the aspartic acid (D) at amino acid position 325 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