rs6938239
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000334441.4(ENSG00000186328):n.246G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.845 in 170,734 control chromosomes in the GnomAD database, including 61,209 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 0.84 ( 53804 hom., cov: 30)
Exomes 𝑓: 0.89 ( 7405 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.14
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 (BayesDel_noAF=-0.72).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000334441.4 | n.246G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.840 AC: 127613AN: 151924Hom.: 53764 Cov.: 30
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GnomAD4 exome AF: 0.888 AC: 16591AN: 18692Hom.: 7405 Cov.: 0 AF XY: 0.892 AC XY: 9293AN XY: 10420
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GnomAD4 genome ? AF: 0.840 AC: 127711AN: 152042Hom.: 53804 Cov.: 30 AF XY: 0.839 AC XY: 62339AN XY: 74318
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at