chr19-10092711-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_031917.3(ANGPTL6):​c.1291G>A​(p.Val431Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

ANGPTL6
NM_031917.3 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.41
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]
SHFL (HGNC:25649): (shiftless antiviral inhibitor of ribosomal frameshifting) This gene is an interferon stimulated gene (ISG) that inhibits viral replication. The encoded protein binds nucleic acids and inhibits programmed -1 ribosomal frameshifting required for translation by many RNA viruses. Viruses inhibited by the protein include Zika virus, dengue virus and the coronaviruses, SARS-CoV and SARS-CoV2. [provided by RefSeq, Aug 2021]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3549891).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANGPTL6NM_031917.3 linkuse as main transcriptc.1291G>A p.Val431Met missense_variant 6/6 ENST00000253109.5
SHFLNM_018381.4 linkuse as main transcriptc.*409C>T 3_prime_UTR_variant 8/8 ENST00000253110.16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANGPTL6ENST00000253109.5 linkuse as main transcriptc.1291G>A p.Val431Met missense_variant 6/61 NM_031917.3 P1
SHFLENST00000253110.16 linkuse as main transcriptc.*409C>T 3_prime_UTR_variant 8/82 NM_018381.4 P1Q9NUL5-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

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 GeneticsAug 30, 2022The c.1291G>A (p.V431M) alteration is located in exon 6 (coding exon 5) of the ANGPTL6 gene. This alteration results from a G to A substitution at nucleotide position 1291, causing the valine (V) at amino acid position 431 to be replaced by a methionine (M). 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
0.17
BayesDel_addAF
Benign
-0.061
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.017
T;T;T
Eigen
Benign
-0.44
Eigen_PC
Benign
-0.41
FATHMM_MKL
Uncertain
0.80
D
LIST_S2
Benign
0.85
D;.;T
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.35
T;T;T
MetaSVM
Benign
-0.65
T
MutationAssessor
Benign
1.4
.;L;L
MutationTaster
Benign
0.99
D;D;D;D;D;D
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-1.8
.;.;N
REVEL
Benign
0.20
Sift
Uncertain
0.012
.;.;D
Sift4G
Uncertain
0.032
D;D;D
Polyphen
0.053
.;B;B
Vest4
0.25
MutPred
0.50
.;Loss of catalytic residue at V431 (P = 0.0045);Loss of catalytic residue at V431 (P = 0.0045);
MVP
0.68
ClinPred
0.73
D
GERP RS
3.4
Varity_R
0.13
gMVP
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.18
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-10203387; API