rs11099864
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001371116.1(FHDC1):c.1219-175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,002 control chromosomes in the GnomAD database, including 30,208 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 0.58 ( 30208 hom., cov: 31)
Consequence
FHDC1
NM_001371116.1 intron
NM_001371116.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.76
Genes affected
FHDC1 (HGNC:29363): (FH2 domain containing 1) Predicted to enable actin binding activity and microtubule binding activity. Involved in Golgi ribbon formation; cilium assembly; and stress fiber assembly. Located in cilium and microtubule. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FHDC1 | NM_001371116.1 | c.1219-175G>A | intron_variant | ENST00000511601.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FHDC1 | ENST00000511601.6 | c.1219-175G>A | intron_variant | 5 | NM_001371116.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.585 AC: 88813AN: 151884Hom.: 30207 Cov.: 31
GnomAD3 genomes
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88813
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.584 AC: 88815AN: 152002Hom.: 30208 Cov.: 31 AF XY: 0.584 AC XY: 43366AN XY: 74318
GnomAD4 genome
?
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88815
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152002
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31
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43366
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74318
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1812
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
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