Variant chr3-52502648-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_015136.3(STAB1):c.504C>T(p.His168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0063 in 1,613,310 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0050 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0064 ( 70 hom. )

Consequence

STAB1
NM_015136.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.79

Variant links:

Genes affected

STAB1 (HGNC:18628): (stabilin 1) This gene encodes a large, transmembrane receptor protein which may function in angiogenesis, lymphocyte homing, cell adhesion, or receptor scavenging. The protein contains 7 fasciclin, 16 epidermal growth factor (EGF)-like, and 2 laminin-type EGF-like domains as well as a C-type lectin-like hyaluronan-binding Link module. The protein is primarily expressed on sinusoidal endothelial cells of liver, spleen, and lymph node. The receptor has been shown to endocytose ligands such as low density lipoprotein, Gram-positive and Gram-negative bacteria, and advanced glycosylation end products. Supporting its possible role as a scavenger receptor, the protein rapidly cycles between the plasma membrane and early endosomes. [provided by RefSeq, Jul 2008]

STAB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 3-52502648-C-T is Benign according to our data. Variant chr3-52502648-C-T is described in ClinVar as [Benign]. Clinvar id is 767910.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.79 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00503 (767/152338) while in subpopulation SAS AF= 0.023 (111/4828). AF 95% confidence interval is 0.0195. There are 4 homozygotes in gnomad4. There are 398 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAB1	NM_015136.3 linkuse as main transcript	c.504C>T	p.His168=	synonymous_variant	6/69	ENST00000321725.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAB1	ENST00000321725.10 linkuse as main transcript	c.504C>T	p.His168=	synonymous_variant	6/69	1	NM_015136.3	P1	Q9NY15-1
STAB1	ENST00000481607.1 linkuse as main transcript	n.559C>T		non_coding_transcript_exon_variant	6/21	1

Frequencies

GnomAD3 genomes

AF:

0.00506

AC:

770

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00499

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00360

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0234

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00525

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00630

AC:

1579

AN:

250594

Hom.:

AF XY:

0.00733

AC XY:

995

AN XY:

135674

show subpopulations

Gnomad AFR exome

AF:

0.00463

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.00159

Gnomad EAS exome

AF:

0.000816

Gnomad SAS exome

AF:

0.0251

Gnomad FIN exome

AF:

0.00171

Gnomad NFE exome

AF:

0.00503

Gnomad OTH exome

AF:

0.00295

GnomAD4 exome

AF:

0.00644

AC:

9402

AN:

1460972

Hom.:

Cov.:

AF XY:

0.00699

AC XY:

5076

AN XY:

726682

show subpopulations

Gnomad4 AFR exome

AF:

0.00505

Gnomad4 AMR exome

AF:

0.00230

Gnomad4 ASJ exome

AF:

0.00161

Gnomad4 EAS exome

AF:

0.000655

Gnomad4 SAS exome

AF:

0.0247

Gnomad4 FIN exome

AF:

0.00162

Gnomad4 NFE exome

AF:

0.00579

Gnomad4 OTH exome

AF:

0.00620

GnomAD4 genome

AF:

0.00503

AC:

767

AN:

152338

Hom.:

Cov.:

AF XY:

0.00534

AC XY:

398

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.00498

Gnomad4 AMR

AF:

0.00359

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0230

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00523

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00460

Hom.:

Bravo

AF:

0.00437

Asia WGS

AF:

0.00866

AC:

AN:

3478

EpiCase

AF:

0.00431

EpiControl

AF:

0.00563

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.48

DANN

Benign

0.30

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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