chr10-122461028-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000650300.1(ENSG00000285955):n.356C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,162 control chromosomes in the GnomAD database, including 4,399 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.23 ( 4399 hom., cov: 34)
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.125
Genes affected
HTRA1 (HGNC:9476): (HtrA serine peptidase 1) This gene encodes a member of the trypsin family of serine proteases. This protein is a secreted enzyme that is proposed to regulate the availability of insulin-like growth factors (IGFs) by cleaving IGF-binding proteins. It has also been suggested to be a regulator of cell growth. Variations in the promoter region of this gene are the cause of susceptibility to age-related macular degeneration type 7. [provided by RefSeq, Jul 2008]
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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 (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105378525 | XR_946382.3 | n.378C>T | non_coding_transcript_exon_variant | 1/3 | |||
LOC105378525 | XR_946383.3 | n.356C>T | non_coding_transcript_exon_variant | 1/4 | |||
LOC105378525 | XR_946384.3 | n.356C>T | non_coding_transcript_exon_variant | 1/4 | |||
LOC105378525 | XR_946385.3 | n.356C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000650300.1 | n.356C>T | non_coding_transcript_exon_variant | 1/3 | ||||||
HTRA1 | ENST00000648167.1 | c.154+2319G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.234 AC: 35620AN: 152042Hom.: 4389 Cov.: 34
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.234 AC: 35666AN: 152162Hom.: 4399 Cov.: 34 AF XY: 0.237 AC XY: 17634AN XY: 74384
GnomAD4 genome
?
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1277
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ClinVar
Significance: risk factor
Submissions summary: Other:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Age related macular degeneration 7 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Feb 18, 2015 | - - |
Susceptibility to neovascular type of age-related macular degeneration Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Feb 18, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at