1-108650337-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001102592.2(HENMT1):c.630C>T(p.Val210=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0037 in 1,613,964 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0038 ( 12 hom. )
Consequence
HENMT1
NM_001102592.2 synonymous
NM_001102592.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.42
Genes affected
HENMT1 (HGNC:26400): (HEN methyltransferase 1) Enables small RNA 2'-O-methyltransferase. Involved in RNA methylation. Predicted to be located in P granule. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 1-108650337-G-A is Benign according to our data. Variant chr1-108650337-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638963.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-6.42 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HENMT1 | NM_001102592.2 | c.630C>T | p.Val210= | synonymous_variant | 7/8 | ENST00000651461.1 | |
HENMT1 | NM_144584.3 | c.630C>T | p.Val210= | synonymous_variant | 7/8 | ||
HENMT1 | XM_005270411.2 | c.654C>T | p.Val218= | synonymous_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HENMT1 | ENST00000651461.1 | c.630C>T | p.Val210= | synonymous_variant | 7/8 | NM_001102592.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00295 AC: 448AN: 152048Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00314 AC: 790AN: 251392Hom.: 4 AF XY: 0.00337 AC XY: 458AN XY: 135852
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GnomAD4 exome AF: 0.00378 AC: 5526AN: 1461798Hom.: 12 Cov.: 31 AF XY: 0.00370 AC XY: 2690AN XY: 727204
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GnomAD4 genome AF: 0.00294 AC: 447AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00312 AC XY: 232AN XY: 74414
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | HENMT1: BP4, BP7 - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at