rs2593813

Positions:

• chr3-186614782-G-A
• chr3-186614782-G-C
• chr3-186614782-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

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
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.115

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)

ACMG classification

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
AHSG	NM_001622.4	c.214-903G>A		intron_variant		ENST00000411641.7
AHSG	NM_001354571.2	c.214-903G>A		intron_variant
AHSG	NM_001354572.2	c.214-906G>A		intron_variant
AHSG	NM_001354573.2	c.214-903G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHSG	ENST00000411641.7	c.214-903G>A		intron_variant		1	NM_001622.4	P3
HRG-AS1	ENST00000630178.2	n.239-34816C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96583 AN: 151918 Hom.: 30905 Cov.: 32

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

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

Submissions by phenotype

RECLASSIFIED - ALPHA-2-HS-GLYCOPROTEIN POLYMORPHISM Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jun 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

Other links and lift over

dbSNP: rs2593813; hg19: chr3-186332571;