rs143399622
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The ENST00000370425.8(HFM1):c.2308G>A(p.Asp770Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00272 in 1,444,094 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0022 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 9 hom. )
Consequence
HFM1
ENST00000370425.8 missense
ENST00000370425.8 missense
Scores
1
9
9
Clinical Significance
Conservation
PhyloP100: 5.64
Genes affected
HFM1 (HGNC:20193): (helicase for meiosis 1) The protein encoded by this gene is thought to be an ATP-dependent DNA helicase and is expressed mainly in germ-line cells. Defects in this gene are a cause of premature ovarian failure 9 (POF9). [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 1-91343457-C-T is Benign according to our data. Variant chr1-91343457-C-T is described in ClinVar as [Benign]. Clinvar id is 435416.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00222 (337/152020) while in subpopulation NFE AF= 0.0041 (279/67990). AF 95% confidence interval is 0.00371. There are 1 homozygotes in gnomad4. There are 142 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HFM1 | NM_001017975.6 | c.2308G>A | p.Asp770Asn | missense_variant | 20/39 | ENST00000370425.8 | NP_001017975.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HFM1 | ENST00000370425.8 | c.2308G>A | p.Asp770Asn | missense_variant | 20/39 | 1 | NM_001017975.6 | ENSP00000359454 | P1 | |
HFM1 | ENST00000430465.1 | c.76G>A | p.Asp26Asn | missense_variant | 2/19 | 1 | ENSP00000387661 | |||
HFM1 | ENST00000462405.5 | n.234G>A | non_coding_transcript_exon_variant | 3/21 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00222 AC: 337AN: 152020Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00184 AC: 370AN: 201368Hom.: 2 AF XY: 0.00195 AC XY: 213AN XY: 109066
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GnomAD4 exome AF: 0.00278 AC: 3595AN: 1292074Hom.: 9 Cov.: 19 AF XY: 0.00270 AC XY: 1744AN XY: 646302
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GnomAD4 genome AF: 0.00222 AC: 337AN: 152020Hom.: 1 Cov.: 32 AF XY: 0.00191 AC XY: 142AN XY: 74266
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 24, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
HFM1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: -27
Find out detailed SpliceAI scores and Pangolin per-transcript scores at