3-186617287-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001622.4(AHSG):c.510C>T(p.Ala170=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000377 in 1,614,226 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 4 hom. )
Consequence
AHSG
NM_001622.4 synonymous
NM_001622.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.177
Genes affected
AHSG (HGNC:349): (alpha 2-HS glycoprotein) The protein encoded by this gene is a negatively-charged serum glycoprotein that is synthesized by hepatocytes. The encoded protein consists of two polypeptide chains, which are both cleaved from a proprotein encoded from a single mRNA. It is involved in several processes, including endocytosis, brain development, and the formation of bone tissue. Defects in this gene are a cause of susceptibility to leanness. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 3-186617287-C-T is Benign according to our data. Variant chr3-186617287-C-T is described in ClinVar as [Benign]. Clinvar id is 790549.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.177 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHSG | NM_001622.4 | c.510C>T | p.Ala170= | synonymous_variant | 4/7 | ENST00000411641.7 | |
AHSG | NM_001354571.2 | c.513C>T | p.Ala171= | synonymous_variant | 4/7 | ||
AHSG | NM_001354572.2 | c.507C>T | p.Ala169= | synonymous_variant | 4/7 | ||
AHSG | NM_001354573.2 | c.510C>T | p.Ala170= | synonymous_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHSG | ENST00000411641.7 | c.510C>T | p.Ala170= | synonymous_variant | 4/7 | 1 | NM_001622.4 | P3 | |
HRG-AS1 | ENST00000630178.2 | n.239-37321G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00188 AC: 286AN: 152222Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000537 AC: 135AN: 251482Hom.: 2 AF XY: 0.000383 AC XY: 52AN XY: 135914
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GnomAD4 exome AF: 0.000220 AC: 321AN: 1461886Hom.: 4 Cov.: 32 AF XY: 0.000227 AC XY: 165AN XY: 727242
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GnomAD4 genome ? AF: 0.00188 AC: 287AN: 152340Hom.: 2 Cov.: 32 AF XY: 0.00187 AC XY: 139AN XY: 74494
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at