Variant rs1071592 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000411641.7(AHSG):c.810A>C(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 (★★).

Frequency

Genomes: 𝑓 0.77 ( 45925 hom., cov: 31)

Exomes 𝑓: 0.75 ( 414400 hom. )

Consequence

AHSG
ENST00000411641.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.399

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:

HRG-AS1 (HGNC:55915): (HRG and FETUB antisense RNA 1)

HRG-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 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_multiple_submitters_no_conflicts, 2 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	Protein
AHSG	NM_001622.4 linkuse as main transcript	c.810A>C	p.Thr270=	synonymous_variant	7/7	ENST00000411641.7	NP_001613.2
AHSG	NM_001354571.2 linkuse as main transcript	c.813A>C	p.Thr271=	synonymous_variant	7/7		NP_001341500.1
AHSG	NM_001354572.2 linkuse as main transcript	c.807A>C	p.Thr269=	synonymous_variant	7/7		NP_001341501.1
AHSG	NM_001354573.2 linkuse as main transcript	c.726A>C	p.Thr242=	synonymous_variant	6/6		NP_001341502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHSG	ENST00000411641.7 linkuse as main transcript	c.810A>C	p.Thr270=	synonymous_variant	7/7	1	NM_001622.4	ENSP00000393887	P3
HRG-AS1	ENST00000630178.2 linkuse as main transcript	n.239-40670T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.775

AC:

117714

AN:

151914

Hom.:

45887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.850

Gnomad AMI

AF:

0.819

Gnomad AMR

AF:

0.692

Gnomad ASJ

AF:

0.836

Gnomad EAS

AF:

0.828

Gnomad SAS

AF:

0.860

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.746

Gnomad OTH

AF:

0.801

GnomAD3 exomes

AF:

0.758

AC:

190315

AN:

250990

Hom.:

73001

AF XY:

0.767

AC XY:

104000

AN XY:

135610

show subpopulations

Gnomad AFR exome

AF:

0.852

Gnomad AMR exome

AF:

0.628

Gnomad ASJ exome

AF:

0.836

Gnomad EAS exome

AF:

0.835

Gnomad SAS exome

AF:

0.858

Gnomad FIN exome

AF:

0.684

Gnomad NFE exome

AF:

0.751

Gnomad OTH exome

AF:

0.774

GnomAD4 exome

AF:

0.751

AC:

1097660

AN:

1460856

Hom.:

414400

Cov.:

AF XY:

0.756

AC XY:

548971

AN XY:

726536

show subpopulations

Gnomad4 AFR exome

AF:

0.849

Gnomad4 AMR exome

AF:

0.637

Gnomad4 ASJ exome

AF:

0.837

Gnomad4 EAS exome

AF:

0.825

Gnomad4 SAS exome

AF:

0.855

Gnomad4 FIN exome

AF:

0.688

Gnomad4 NFE exome

AF:

0.741

Gnomad4 OTH exome

AF:

0.777

GnomAD4 genome

AF:

0.775

AC:

117807

AN:

152032

Hom.:

45925

Cov.:

AF XY:

0.773

AC XY:

57417

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.850

Gnomad4 AMR

AF:

0.692

Gnomad4 ASJ

AF:

0.836

Gnomad4 EAS

AF:

0.827

Gnomad4 SAS

AF:

0.860

Gnomad4 FIN

AF:

0.686

Gnomad4 NFE

AF:

0.746

Gnomad4 OTH

AF:

0.801

Alfa

AF:

0.770

Hom.:

23748

Bravo

AF:

0.779

Asia WGS

AF:

0.821

AC:

2855

AN:

3478

EpiCase

AF:

0.773

EpiControl

AF:

0.775

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.96

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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