19-10093854-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_031917.3(ANGPTL6):​c.790C>T​(p.Arg264Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000251 in 1,610,612 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00026 ( 1 hom. )

Consequence

ANGPTL6
NM_031917.3 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.15
Variant links:
Genes affected
ANGPTL6 (HGNC:23140): (angiopoietin like 6) Predicted to enable signaling receptor binding activity. Predicted to be involved in angiogenesis and cell differentiation. Located in extracellular exosome. Part of collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.024825573).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANGPTL6NM_031917.3 linkuse as main transcriptc.790C>T p.Arg264Cys missense_variant 4/6 ENST00000253109.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANGPTL6ENST00000253109.5 linkuse as main transcriptc.790C>T p.Arg264Cys missense_variant 4/61 NM_031917.3 P1
ANGPTL6ENST00000592641.5 linkuse as main transcriptc.790C>T p.Arg264Cys missense_variant 4/61 P1
ANGPTL6ENST00000589181.5 linkuse as main transcriptc.790C>T p.Arg264Cys missense_variant 3/55

Frequencies

GnomAD3 genomes
AF:
0.000184
AC:
28
AN:
152228
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00122
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000214
AC:
53
AN:
248066
Hom.:
0
AF XY:
0.000276
AC XY:
37
AN XY:
134300
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.0000993
Gnomad EAS exome
AF:
0.000218
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00114
Gnomad NFE exome
AF:
0.000202
Gnomad OTH exome
AF:
0.000164
GnomAD4 exome
AF:
0.000259
AC:
377
AN:
1458266
Hom.:
1
Cov.:
31
AF XY:
0.000274
AC XY:
199
AN XY:
725580
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.000802
Gnomad4 NFE exome
AF:
0.000283
Gnomad4 OTH exome
AF:
0.000215
GnomAD4 genome
AF:
0.000184
AC:
28
AN:
152346
Hom.:
0
Cov.:
32
AF XY:
0.000242
AC XY:
18
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.0000653
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00122
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000163
Hom.:
0
Bravo
AF:
0.000147
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000519
AC:
2
ExAC
AF:
0.000214
AC:
26
EpiCase
AF:
0.000164
EpiControl
AF:
0.0000593

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 01, 2021The c.790C>T (p.R264C) alteration is located in exon 4 (coding exon 3) of the ANGPTL6 gene. This alteration results from a C to T substitution at nucleotide position 790, causing the arginine (R) at amino acid position 264 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
19
DANN
Uncertain
1.0
DEOGEN2
Benign
0.035
T;T;T
Eigen
Benign
-0.45
Eigen_PC
Benign
-0.59
FATHMM_MKL
Benign
0.18
N
LIST_S2
Benign
0.80
T;.;T
M_CAP
Uncertain
0.15
D
MetaRNN
Benign
0.025
T;T;T
MetaSVM
Benign
-0.77
T
MutationAssessor
Benign
1.2
.;L;L
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.22
T
PROVEAN
Benign
-1.6
.;.;N
REVEL
Benign
0.19
Sift
Uncertain
0.022
.;.;D
Sift4G
Uncertain
0.015
D;D;D
Polyphen
0.88
.;P;P
Vest4
0.30
MVP
0.70
ClinPred
0.047
T
GERP RS
2.4
Varity_R
0.12
gMVP
0.35

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.

Other links and lift over

dbSNP: rs182345321; hg19: chr19-10204530; API