rs299284
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000520345(HMMR):c.-69C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.105 in 1,605,700 control chromosomes in the GnomAD database, including 9,376 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 0.10 ( 852 hom., cov: 32)
Exomes 𝑓: 0.11 ( 8524 hom. )
Consequence
HMMR
ENST00000520345 5_prime_UTR_premature_start_codon_gain
ENST00000520345 5_prime_UTR_premature_start_codon_gain
Scores
5
6
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.93
Genes affected
HMMR (HGNC:5012): (hyaluronan mediated motility receptor) The protein encoded by this gene is involved in cell motility. It is expressed in breast tissue and together with other proteins, it forms a complex with BRCA1 and BRCA2, thus is potentially associated with higher risk of breast cancer. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMMR | NM_001142556.2 | c.277C>T | p.Arg93Cys | missense_variant | 5/18 | ENST00000393915.9 | NP_001136028.1 | |
HMMR | NM_012484.3 | c.274C>T | p.Arg92Cys | missense_variant | 5/18 | NP_036616.2 | ||
HMMR | NM_012485.3 | c.229C>T | p.Arg77Cys | missense_variant | 4/17 | NP_036617.2 | ||
HMMR | NM_001142557.2 | c.16C>T | p.Arg6Cys | missense_variant | 2/15 | NP_001136029.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HMMR | ENST00000520345 | c.-69C>T | 5_prime_UTR_premature_start_codon_gain_variant | 4/6 | 2 | ENSP00000428481.1 | ||||
HMMR | ENST00000393915.9 | c.277C>T | p.Arg93Cys | missense_variant | 5/18 | 1 | NM_001142556.2 | ENSP00000377492.4 | ||
HMMR | ENST00000520345 | c.-69C>T | 5_prime_UTR_variant | 4/6 | 2 | ENSP00000428481.1 |
Frequencies
GnomAD3 genomes AF: 0.103 AC: 15590AN: 152000Hom.: 855 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0992 AC: 24368AN: 245592Hom.: 1404 AF XY: 0.102 AC XY: 13576AN XY: 132980
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GnomAD4 exome AF: 0.106 AC: 153415AN: 1453582Hom.: 8524 Cov.: 30 AF XY: 0.106 AC XY: 76730AN XY: 723380
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GnomAD4 genome AF: 0.102 AC: 15588AN: 152118Hom.: 852 Cov.: 32 AF XY: 0.103 AC XY: 7647AN XY: 74346
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390
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421
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
.;.;.;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;D;D;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;.;M
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
D;D;D;D
Vest4
MPC
0.42
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 15
Find out detailed SpliceAI scores and Pangolin per-transcript scores at