rs299290
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142556.2(HMMR):c.1106T>A(p.Val369Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HMMR
NM_001142556.2 missense
NM_001142556.2 missense
Scores
1
16
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0270
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.052818567).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HMMR | NM_001142556.2 | c.1106T>A | p.Val369Asp | missense_variant | 11/18 | ENST00000393915.9 | |
HMMR | NM_012484.3 | c.1103T>A | p.Val368Asp | missense_variant | 11/18 | ||
HMMR | NM_012485.3 | c.1058T>A | p.Val353Asp | missense_variant | 10/17 | ||
HMMR | NM_001142557.2 | c.845T>A | p.Val282Asp | missense_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMMR | ENST00000393915.9 | c.1106T>A | p.Val369Asp | missense_variant | 11/18 | 1 | NM_001142556.2 | A2 | |
HMMR | ENST00000358715.3 | c.1103T>A | p.Val368Asp | missense_variant | 11/18 | 1 | P4 | ||
HMMR | ENST00000353866.7 | c.1058T>A | p.Val353Asp | missense_variant | 10/17 | 1 | |||
HMMR | ENST00000432118.6 | c.845T>A | p.Val282Asp | missense_variant | 8/15 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1457302Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 725358
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1457302
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
725358
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
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Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
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Gnomad4 NFE exome
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Gnomad4 OTH exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Benign
T;T;T;T
Polyphen
B;B;B;B
Vest4
MutPred
0.093
.;.;.;Loss of methylation at K369 (P = 0.0431);
MVP
MPC
0.10
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at