chr10-37219522-A-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_052997.3(ANKRD30A):āc.3810A>Gā(p.Ala1270Ala) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control
Consequence
ANKRD30A
NM_052997.3 synonymous
NM_052997.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.650
Genes affected
ANKRD30A (HGNC:17234): (ankyrin repeat domain 30A) This gene encodes a DNA-binding transcription factor that is uniquely expressed in mammary epithelium and the testis. Altered expression levels have been associated with breast cancer progression. [provided by RefSeq, Nov 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP7
Synonymous conserved (PhyloP=-0.65 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD30A | ENST00000361713.2 | c.3810A>G | p.Ala1270Ala | synonymous_variant | 34/36 | 5 | NM_052997.3 | ENSP00000354432.2 | ||
ANKRD30A | ENST00000374660.7 | c.4167A>G | p.Ala1389Ala | synonymous_variant | 40/42 | 5 | ENSP00000363792.2 | |||
ANKRD30A | ENST00000602533.7 | c.3810A>G | p.Ala1270Ala | synonymous_variant | 34/36 | 5 | ENSP00000473551.2 | |||
ANKRD30A | ENST00000696674.1 | c.543A>G | p.Ala181Ala | synonymous_variant | 1/2 | ENSP00000512798.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 150676Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 genomes
AF:
AC:
0
AN:
150676
Hom.:
Cov.:
31
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Cov.: 67
GnomAD4 exome
Cov.:
67
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 150676Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73552
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
150676
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
73552
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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