Variant 3-186613180-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001622.4(AHSG):c.39C>G(p.Leu13Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,613,722 control chromosomes in the GnomAD database, including 21,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.19 ( 3506 hom., cov: 31)

Exomes 𝑓: 0.15 ( 17803 hom. )

Consequence

AHSG
NM_001622.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.124

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]

AHSG links:

AHSG (HGNC:):

AHSG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 3-186613180-C-G is Benign according to our data. Variant chr3-186613180-C-G is described in ClinVar as [Benign]. Clinvar id is 3058930.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.124 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHSG	NM_001622.4 linkuse as main transcript	c.39C>G	p.Leu13Leu	synonymous_variant	1/7	ENST00000411641.7	NP_001613.2	P02765
AHSG	NM_001354571.2 linkuse as main transcript	c.39C>G	p.Leu13Leu	synonymous_variant	1/7		NP_001341500.1
AHSG	NM_001354572.2 linkuse as main transcript	c.39C>G	p.Leu13Leu	synonymous_variant	1/7		NP_001341501.1
AHSG	NM_001354573.2 linkuse as main transcript	c.39C>G	p.Leu13Leu	synonymous_variant	1/6		NP_001341502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHSG	ENST00000411641.7 linkuse as main transcript	c.39C>G	p.Leu13Leu	synonymous_variant	1/7	1	NM_001622.4	ENSP00000393887.2		P02765

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29543

AN:

151920

Hom.:

3500

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.0958

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.216

GnomAD3 exomes

AF:

0.158

AC:

39644

AN:

251210

Hom.:

3701

AF XY:

0.158

AC XY:

21416

AN XY:

135802

show subpopulations

Gnomad AFR exome

AF:

0.336

Gnomad AMR exome

AF:

0.127

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.113

Gnomad SAS exome

AF:

0.212

Gnomad FIN exome

AF:

0.0955

Gnomad NFE exome

AF:

0.139

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.149

AC:

218115

AN:

1461684

Hom.:

17803

Cov.:

AF XY:

0.150

AC XY:

109076

AN XY:

727162

show subpopulations

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.133

Gnomad4 ASJ exome

AF:

0.240

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.0922

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.163

GnomAD4 genome

AF:

0.194

AC:

29560

AN:

152038

Hom.:

3506

Cov.:

AF XY:

0.191

AC XY:

14177

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.174

Gnomad4 ASJ

AF:

0.247

Gnomad4 EAS

AF:

0.122

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.0958

Gnomad4 NFE

AF:

0.136

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.163

Hom.:

775

Bravo

AF:

0.206

Asia WGS

AF:

0.167

AC:

580

AN:

3478

EpiCase

AF:

0.146

EpiControl

AF:

0.157

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

AHSG-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 29, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

9.9

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over