chr6-30949470-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_080870.4(MUCL3):c.1006G>A(p.Ala336Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000858 in 106,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_080870.4 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 |
---|---|---|---|---|---|---|---|
MUCL3 | NM_080870.4 | c.1006G>A | p.Ala336Thr | missense_variant | 2/3 | ENST00000462446.6 | |
HCG21 | NR_138040.1 | n.256+2892C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUCL3 | ENST00000462446.6 | c.1006G>A | p.Ala336Thr | missense_variant | 2/3 | 5 | NM_080870.4 | A2 | |
HCG21 | ENST00000419481.1 | n.225-3111C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
MUCL3 | ENST00000636043.1 | c.1207G>A | p.Ala403Thr | missense_variant | 5/6 | 5 | P4 | ||
SFTA2 | ENST00000634371.1 | c.-9+2892C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000859 AC: 91AN: 105944Hom.: 0 Cov.: 27
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000347 AC: 441AN: 1271446Hom.: 0 Cov.: 164 AF XY: 0.000364 AC XY: 227AN XY: 623482
GnomAD4 genome ? AF: 0.000858 AC: 91AN: 106038Hom.: 0 Cov.: 27 AF XY: 0.000827 AC XY: 42AN XY: 50816
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 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