18-54331820-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_139171.2(STARD6):c.307G>A(p.Val103Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,612,828 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V103L) has been classified as Uncertain significance.
Frequency
Consequence
NM_139171.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STARD6 | NM_139171.2 | c.307G>A | p.Val103Met | missense_variant | 6/8 | ENST00000307844.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STARD6 | ENST00000307844.4 | c.307G>A | p.Val103Met | missense_variant | 6/8 | 1 | NM_139171.2 | P2 | |
STARD6 | ENST00000686109.1 | c.340G>A | p.Val114Met | missense_variant | 7/9 | A2 | |||
STARD6 | ENST00000581310.5 | c.307G>A | p.Val103Met | missense_variant | 7/9 | 5 | P2 | ||
STARD6 | ENST00000689888.1 | c.*363G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251188Hom.: 1 AF XY: 0.000103 AC XY: 14AN XY: 135752
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1460770Hom.: 1 Cov.: 29 AF XY: 0.0000674 AC XY: 49AN XY: 726656
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74276
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at