rs17194931
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003878.3(GGH):c.225-1568C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,222 control chromosomes in the GnomAD database, including 437 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 0.071 ( 437 hom., cov: 32)
Consequence
GGH
NM_003878.3 intron
NM_003878.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.286
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=-0.89).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GGH | NM_003878.3 | c.225-1568C>T | intron_variant | ENST00000260118.7 | |||
GGH | NM_001410926.1 | c.225-1568C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GGH | ENST00000260118.7 | c.225-1568C>T | intron_variant | 1 | NM_003878.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0712 AC: 10832AN: 152104Hom.: 435 Cov.: 32
GnomAD3 genomes
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152104
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0712 AC: 10831AN: 152222Hom.: 437 Cov.: 32 AF XY: 0.0710 AC XY: 5281AN XY: 74416
GnomAD4 genome
?
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10831
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152222
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32
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5281
AN XY:
74416
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Asia WGS
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401
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at