rs3757340
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080870.4(MUCL3):c.*988T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,122 control chromosomes in the GnomAD database, including 10,700 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 10697 hom., cov: 31)
Exomes 𝑓: 0.29 ( 3 hom. )
Consequence
MUCL3
NM_080870.4 3_prime_UTR
NM_080870.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.497
Genes affected
MUCL3 (HGNC:21666): (mucin like 3) Predicted to be located in cytoplasm and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUCL3 | NM_080870.4 | c.*988T>C | 3_prime_UTR_variant | 3/3 | ENST00000462446.6 | ||
HCG21 | NR_138040.1 | n.86+672A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUCL3 | ENST00000462446.6 | c.*988T>C | 3_prime_UTR_variant | 3/3 | 5 | NM_080870.4 | A2 | ||
HCG21 | ENST00000419481.1 | n.86+672A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
MUCL3 | ENST00000636043.1 | c.*988T>C | 3_prime_UTR_variant | 6/6 | 5 | P4 | |||
SFTA2 | ENST00000634371.1 | c.-326+672A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.364 AC: 55291AN: 151946Hom.: 10673 Cov.: 31
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GnomAD4 exome AF: 0.293 AC: 17AN: 58Hom.: 3 Cov.: 0 AF XY: 0.321 AC XY: 9AN XY: 28
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GnomAD4 genome ? AF: 0.364 AC: 55354AN: 152064Hom.: 10697 Cov.: 31 AF XY: 0.372 AC XY: 27650AN XY: 74318
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at