Variant chr11-101905796-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_178127.5(ANGPTL5):c.293T>C(p.Leu98Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00192 in 1,612,358 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0016 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0020 ( 25 hom. )

Consequence

ANGPTL5
NM_178127.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 6.86

Variant links:

Genes affected

ANGPTL5 (HGNC:19705): (angiopoietin like 5) Predicted to be active in collagen-containing extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ANGPTL5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008781582).

BP6

Variant 11-101905796-A-G is Benign according to our data. Variant chr11-101905796-A-G is described in ClinVar as [Benign]. Clinvar id is 709088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ANGPTL5	NM_178127.5 linkuse as main transcript	c.293T>C	p.Leu98Pro	missense_variant	4/9	ENST00000334289.7	NP_835228.2
ANGPTL5	XM_011542735.4 linkuse as main transcript	c.293T>C	p.Leu98Pro	missense_variant	4/7		XP_011541037.1
ANGPTL5	XM_017017466.3 linkuse as main transcript	c.241+1307T>C		intron_variant			XP_016872955.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANGPTL5	ENST00000334289.7 linkuse as main transcript	c.293T>C	p.Leu98Pro	missense_variant	4/9	1	NM_178127.5	ENSP00000335255	P1
ANGPTL5	ENST00000534527.1 linkuse as main transcript	c.293T>C	p.Leu98Pro	missense_variant	3/5	3		ENSP00000433562

Frequencies

GnomAD3 genomes

AF:

0.00158

AC:

240

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000506

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00223

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00712

Gnomad SAS

AF:

0.0145

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000897

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00450

AC:

1127

AN:

250610

Hom.:

AF XY:

0.00449

AC XY:

608

AN XY:

135498

show subpopulations

Gnomad AFR exome

AF:

0.000740

Gnomad AMR exome

AF:

0.0100

Gnomad ASJ exome

AF:

0.00586

Gnomad EAS exome

AF:

0.00544

Gnomad SAS exome

AF:

0.0145

Gnomad FIN exome

AF:

0.0000468

Gnomad NFE exome

AF:

0.00123

Gnomad OTH exome

AF:

0.00475

GnomAD4 exome

AF:

0.00195

AC:

2854

AN:

1460038

Hom.:

Cov.:

AF XY:

0.00217

AC XY:

1574

AN XY:

726406

show subpopulations

Gnomad4 AFR exome

AF:

0.00135

Gnomad4 AMR exome

AF:

0.00871

Gnomad4 ASJ exome

AF:

0.00590

Gnomad4 EAS exome

AF:

0.00389

Gnomad4 SAS exome

AF:

0.0137

Gnomad4 FIN exome

AF:

0.0000567

Gnomad4 NFE exome

AF:

0.000626

Gnomad4 OTH exome

AF:

0.00297

GnomAD4 genome

AF:

0.00157

AC:

239

AN:

152320

Hom.:

Cov.:

AF XY:

0.00169

AC XY:

126

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.000505

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.00694

Gnomad4 SAS

AF:

0.0145

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000897

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00159

Hom.:

Bravo

AF:

0.00181

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00105

AC:

ExAC

AF:

0.00432

AC:

525

Asia WGS

AF:

0.0160

AC:

AN:

3472

EpiCase

AF:

0.00142

EpiControl

AF:

0.00213

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 28, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.88

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Uncertain

-0.020

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.11

T;.

Eigen

Uncertain

0.61

Eigen_PC

Uncertain

0.61

FATHMM_MKL

Uncertain

0.97

LIST_S2

Benign

0.77

T;T

MetaRNN

Benign

0.0088

T;T

MetaSVM

Benign

-0.45

MutationAssessor

Benign

0.69

N;.

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.71

PROVEAN

Benign

-2.3

N;N

REVEL

Benign

0.27

Sift

Uncertain

0.0020

D;T

Sift4G

Uncertain

0.0020

D;D

Polyphen

1.0

D;.

Vest4

0.72

MVP

0.63

MPC

0.068

ClinPred

0.030

GERP RS

5.1

Varity_R

0.76

gMVP

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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