rs2593813

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001622.4(AHSG):​c.214-903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,036 control chromosomes in the GnomAD database, including 30,916 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.64 ( 30916 hom., cov: 32)

Consequence

AHSG
NM_001622.4 intron

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.115
Variant links:
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]
HRG-AS1 (HGNC:55915): (HRG and FETUB antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 3-186614782-G-A is Benign according to our data. Variant chr3-186614782-G-A is described in ClinVar as [Benign]. Clinvar id is 16045.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AHSGNM_001622.4 linkuse as main transcriptc.214-903G>A intron_variant ENST00000411641.7
AHSGNM_001354571.2 linkuse as main transcriptc.214-903G>A intron_variant
AHSGNM_001354572.2 linkuse as main transcriptc.214-906G>A intron_variant
AHSGNM_001354573.2 linkuse as main transcriptc.214-903G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AHSGENST00000411641.7 linkuse as main transcriptc.214-903G>A intron_variant 1 NM_001622.4 P3
HRG-AS1ENST00000630178.2 linkuse as main transcriptn.239-34816C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.636
AC:
96583
AN:
151918
Hom.:
30905
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.612
Gnomad AMI
AF:
0.560
Gnomad AMR
AF:
0.603
Gnomad ASJ
AF:
0.761
Gnomad EAS
AF:
0.723
Gnomad SAS
AF:
0.761
Gnomad FIN
AF:
0.570
Gnomad MID
AF:
0.839
Gnomad NFE
AF:
0.644
Gnomad OTH
AF:
0.690
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.636
AC:
96636
AN:
152036
Hom.:
30916
Cov.:
32
AF XY:
0.636
AC XY:
47234
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.612
Gnomad4 AMR
AF:
0.603
Gnomad4 ASJ
AF:
0.761
Gnomad4 EAS
AF:
0.723
Gnomad4 SAS
AF:
0.762
Gnomad4 FIN
AF:
0.570
Gnomad4 NFE
AF:
0.644
Gnomad4 OTH
AF:
0.689
Alfa
AF:
0.660
Hom.:
43955
Bravo
AF:
0.636
Asia WGS
AF:
0.704
AC:
2448
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

RECLASSIFIED - ALPHA-2-HS-GLYCOPROTEIN POLYMORPHISM Benign:1
Benign, no assertion criteria providedliterature onlyOMIMJun 01, 2005- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.2
DANN
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2593813; hg19: chr3-186332571; API