Variant 3-52502994-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_015136.3(STAB1):c.584-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00626 in 1,563,412 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0066 ( 12 hom., cov: 33)

Exomes 𝑓: 0.0062 ( 86 hom. )

Consequence

STAB1
NM_015136.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0001247

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.19

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 3-52502994-C-T is Benign according to our data. Variant chr3-52502994-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2653890.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-52502994-C-T is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAB1	NM_015136.3 linkuse as main transcript	c.584-5C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000321725.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAB1	ENST00000321725.10 linkuse as main transcript	c.584-5C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_015136.3	P1	Q9NY15-1
STAB1	ENST00000481607.1 linkuse as main transcript	n.639-5C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00664

AC:

1011

AN:

152228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000989

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00311

Gnomad FIN

AF:

0.0505

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00561

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00732

AC:

1387

AN:

189582

Hom.:

AF XY:

0.00758

AC XY:

771

AN XY:

101702

show subpopulations

Gnomad AFR exome

AF:

0.000835

Gnomad AMR exome

AF:

0.00214

Gnomad ASJ exome

AF:

0.000513

Gnomad EAS exome

AF:

0.000133

Gnomad SAS exome

AF:

0.00469

Gnomad FIN exome

AF:

0.0486

Gnomad NFE exome

AF:

0.00488

Gnomad OTH exome

AF:

0.00720

GnomAD4 exome

AF:

0.00622

AC:

8775

AN:

1411066

Hom.:

Cov.:

AF XY:

0.00620

AC XY:

4317

AN XY:

696780

show subpopulations

Gnomad4 AFR exome

AF:

0.000981

Gnomad4 AMR exome

AF:

0.00205

Gnomad4 ASJ exome

AF:

0.000909

Gnomad4 EAS exome

AF:

0.0000528

Gnomad4 SAS exome

AF:

0.00503

Gnomad4 FIN exome

AF:

0.0436

Gnomad4 NFE exome

AF:

0.00529

Gnomad4 OTH exome

AF:

0.00584

GnomAD4 genome

AF:

0.00664

AC:

1012

AN:

152346

Hom.:

Cov.:

AF XY:

0.00840

AC XY:

626

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.000986

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.0505

Gnomad4 NFE

AF:

0.00562

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00424

Hom.:

Bravo

AF:

0.00312

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

STAB1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

9.1

DANN

Benign

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00012

dbscSNV1_RF

Benign

0.0

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