rs12770170
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001378785.1(MSANTD7):c.*3013T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MSANTD7
NM_001378785.1 3_prime_UTR
NM_001378785.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.35
Genes affected
MSANTD7 (HGNC:56248): (Myb/SANT DNA binding domain containing 7)
HSPA14 (HGNC:29526): (heat shock protein family A (Hsp70) member 14) Predicted to enable several functions, including ATP binding activity; misfolded protein binding activity; and unfolded protein binding activity. Predicted to be involved in several processes, including cellular response to unfolded protein; chaperone cofactor-dependent protein refolding; and protein refolding. Located in cytosol. Colocalizes with ribosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSANTD7 | NM_001378785.1 | c.*3013T>C | 3_prime_UTR_variant | 5/5 | ENST00000640019.3 | ||
HSPA14 | NM_016299.4 | c.222-1702T>C | intron_variant | ENST00000378372.8 | |||
MSANTD7 | NM_001378790.1 | c.*3013T>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSANTD7 | ENST00000640019.3 | c.*3013T>C | 3_prime_UTR_variant | 5/5 | 1 | NM_001378785.1 | P1 | ||
HSPA14 | ENST00000378372.8 | c.222-1702T>C | intron_variant | 1 | NM_016299.4 | P1 | |||
HSPA14 | ENST00000441647.1 | c.188-1702T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 833076Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 384712
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
833076
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
384712
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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