chr2-135787878-AAC-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002299.4(LCT):c.*444_*445del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 180,422 control chromosomes in the GnomAD database, including 3,397 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.19 ( 2915 hom., cov: 28)
Exomes 𝑓: 0.16 ( 482 hom. )
Consequence
LCT
NM_002299.4 3_prime_UTR
NM_002299.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.04
Genes affected
LCT (HGNC:6530): (lactase) The protein encoded by this gene belongs to the glycosyl hydrolase 1 family of proteins. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme is integral to the plasma membrane and has both phlorizin hydrolase activity and lactase activity. Mutations in this gene are associated with congenital lactase deficiency. Polymorphisms in this gene are associated with lactase persistence, in which intestinal lactase activity persists at childhood levels into adulthood. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 2-135787878-AAC-A is Benign according to our data. Variant chr2-135787878-AAC-A is described in ClinVar as [Likely_benign]. Clinvar id is 331154.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCT | NM_002299.4 | c.*444_*445del | 3_prime_UTR_variant | 17/17 | ENST00000264162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCT | ENST00000264162.7 | c.*444_*445del | 3_prime_UTR_variant | 17/17 | 1 | NM_002299.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.186 AC: 28325AN: 152032Hom.: 2917 Cov.: 28
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GnomAD4 exome AF: 0.163 AC: 4619AN: 28272Hom.: 482 AF XY: 0.169 AC XY: 2562AN XY: 15120
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GnomAD4 genome AF: 0.186 AC: 28338AN: 152150Hom.: 2915 Cov.: 28 AF XY: 0.188 AC XY: 13994AN XY: 74390
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lactose intolerance Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Congenital lactase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at