3-186614782-G-A

Variant names:

• chr3-186614782-G-A
• rs2593813
• NM_001622.4:c.214-903G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001622.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHSG	NM_001622.4	MANE Select	c.214-903G>A		intron	N/A	NP_001613.2
	AHSG	NM_001354571.2		c.214-903G>A		intron	N/A	NP_001341500.1
	AHSG	NM_001354572.2		c.214-906G>A		intron	N/A	NP_001341501.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHSG	ENST00000411641.7	TSL:1 MANE Select	c.214-903G>A		intron	N/A	ENSP00000393887.2
	AHSG	ENST00000273784.5	TSL:3	c.214-903G>A		intron	N/A	ENSP00000273784.5
	AHSG	ENST00000478441.1	TSL:2	n.271-903G>A		intron	N/A

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

African (AFR) AF: 0.612 AC: 25376 AN: 41454

American (AMR) AF: 0.603 AC: 9210 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3745 AN: 5182

South Asian (SAS) AF: 0.762 AC: 3675 AN: 4824

European-Finnish (FIN) AF: 0.570 AC: 6006 AN: 10542

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43766 AN: 67968

Other (OTH) AF: 0.689 AC: 1458 AN: 2116

Alfa AF: 0.656 Hom.: 55134

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 - AHSG POLYMORPHISM Benign:1

Jun 01, 2005

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2593813; hg19: chr3-186332571;