3-130379592-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001278298.2(COL6A5):āc.842A>Gā(p.Asn281Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,399,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001278298.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A5 | NM_001278298.2 | c.842A>G | p.Asn281Ser | missense_variant | 4/41 | ENST00000373157.9 | NP_001265227.1 | |
COL6A5 | NM_153264.7 | c.842A>G | p.Asn281Ser | missense_variant | 4/40 | NP_694996.5 | ||
COL6A5 | NR_022012.3 | n.1180A>G | non_coding_transcript_exon_variant | 4/42 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL6A5 | ENST00000373157.9 | c.842A>G | p.Asn281Ser | missense_variant | 4/41 | 2 | NM_001278298.2 | ENSP00000362250 | P2 | |
COL6A5 | ENST00000312481.11 | c.842A>G | p.Asn281Ser | missense_variant, NMD_transcript_variant | 4/42 | 1 | ENSP00000309762 | |||
COL6A5 | ENST00000512836.6 | c.842A>G | p.Asn281Ser | missense_variant | 4/40 | 2 | ENSP00000422898 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000650 AC: 1AN: 153834Hom.: 0 AF XY: 0.0000123 AC XY: 1AN XY: 81618
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1399212Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1AN XY: 690120
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | 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