rs1071592
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001622.4(AHSG):āc.810A>Cā(p.Thr270=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 1,612,888 control chromosomes in the GnomAD database, including 460,325 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.77 ( 45925 hom., cov: 31)
Exomes š: 0.75 ( 414400 hom. )
Consequence
AHSG
NM_001622.4 synonymous
NM_001622.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.399
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 3-186620636-A-C is Benign according to our data. Variant chr3-186620636-A-C is described in ClinVar as [Benign]. Clinvar id is 1188909.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.399 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHSG | NM_001622.4 | c.810A>C | p.Thr270= | synonymous_variant | 7/7 | ENST00000411641.7 | |
AHSG | NM_001354571.2 | c.813A>C | p.Thr271= | synonymous_variant | 7/7 | ||
AHSG | NM_001354572.2 | c.807A>C | p.Thr269= | synonymous_variant | 7/7 | ||
AHSG | NM_001354573.2 | c.726A>C | p.Thr242= | synonymous_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHSG | ENST00000411641.7 | c.810A>C | p.Thr270= | synonymous_variant | 7/7 | 1 | NM_001622.4 | P3 | |
HRG-AS1 | ENST00000630178.2 | n.239-40670T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.775 AC: 117714AN: 151914Hom.: 45887 Cov.: 31
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GnomAD3 exomes AF: 0.758 AC: 190315AN: 250990Hom.: 73001 AF XY: 0.767 AC XY: 104000AN XY: 135610
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GnomAD4 exome AF: 0.751 AC: 1097660AN: 1460856Hom.: 414400 Cov.: 66 AF XY: 0.756 AC XY: 548971AN XY: 726536
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GnomAD4 genome ? AF: 0.775 AC: 117807AN: 152032Hom.: 45925 Cov.: 31 AF XY: 0.773 AC XY: 57417AN XY: 74288
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Alopecia-intellectual disability syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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Name
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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