6-30986374-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010909.5(MUC21):c.199G>A(p.Val67Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000308 in 1,558,558 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010909.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC21 | NM_001010909.5 | c.199G>A | p.Val67Met | missense_variant | 2/3 | ENST00000376296.3 | |
MUC21 | NR_130720.3 | n.582G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC21 | ENST00000376296.3 | c.199G>A | p.Val67Met | missense_variant | 2/3 | 1 | NM_001010909.5 | P1 | |
MUC21 | ENST00000486149.2 | c.-1164G>A | 5_prime_UTR_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000999 AC: 14AN: 140094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000996 AC: 25AN: 250910Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135600
GnomAD4 exome AF: 0.000329 AC: 466AN: 1418464Hom.: 0 Cov.: 35 AF XY: 0.000309 AC XY: 218AN XY: 705772
GnomAD4 genome AF: 0.0000999 AC: 14AN: 140094Hom.: 0 Cov.: 32 AF XY: 0.000103 AC XY: 7AN XY: 68258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.199G>A (p.V67M) alteration is located in exon 2 (coding exon 2) of the MUC21 gene. This alteration results from a G to A substitution at nucleotide position 199, causing the valine (V) at amino acid position 67 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