10-62655424-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000647733.1(ENSG00000285837):c.1130-972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,613,968 control chromosomes in the GnomAD database, including 475,776 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 0.81 ( 50907 hom., cov: 31)
Exomes 𝑓: 0.76 ( 424869 hom. )
Consequence
ENSG00000285837
ENST00000647733.1 intron
ENST00000647733.1 intron
Scores
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.25
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=6.7336487E-7).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC124902436 | XM_047426121.1 | c.340A>G | p.Thr114Ala | missense_variant | Exon 3 of 6 | XP_047282077.1 | ||
LOC124902436 | XM_047426118.1 | c.340A>G | p.Thr114Ala | missense_variant | Exon 3 of 6 | XP_047282074.1 | ||
LOC124902436 | XM_047426119.1 | c.340A>G | p.Thr114Ala | missense_variant | Exon 3 of 5 | XP_047282075.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000285837 | ENST00000647733.1 | c.1130-972A>G | intron_variant | Intron 5 of 7 | ENSP00000502188.1 |
Frequencies
GnomAD3 genomes AF: 0.812 AC: 123385AN: 151986Hom.: 50848 Cov.: 31
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GnomAD3 exomes AF: 0.797 AC: 200272AN: 251422Hom.: 80675 AF XY: 0.791 AC XY: 107479AN XY: 135886
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GnomAD4 exome AF: 0.760 AC: 1110768AN: 1461864Hom.: 424869 Cov.: 68 AF XY: 0.761 AC XY: 553436AN XY: 727232
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GnomAD4 genome AF: 0.812 AC: 123501AN: 152104Hom.: 50907 Cov.: 31 AF XY: 0.813 AC XY: 60465AN XY: 74362
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ESP6500AA
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
Sift4G
Benign
T
Vest4
ClinPred
T
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at